Methods for creating integration-free, virus-free, exogenous oncogene-free ips cells and compositions for use in such methods

ABSTRACT

Methods are disclosed for reprogramming a somatic cell, including an adherent cell and a cell in suspension, into an induced pluripotent stem comprising expressing exogenous Sox-2, exogenous Klf-4, exogenous Oct3/4 from DNA that has not integrated into the genome of the somatic cell, suppressing p53 activity within the somatic cell, and exposing the somatic cell to reprogramming-assistance factors comprising an exogenous Alk-5 inhibitor, an exogenous histone deacetylase inhibitor, and an exogenous activator of glycolysis. Compositions and kits for use in such methods are also disclosed as are cells made by such a method.

This application is a Continuation of U.S. application Ser. No. 15/954,291, filed Apr. 16, 2018, the entire disclosure of which is incorporated herein by reference in its entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Mar. 23, 2018, is named P53616_SL.txt and is 62,299 bytes in size.

BACKGROUND OF THE INVENTION

Chronic disease from degenerative organ dysfunction accounts for eighty-six percent of the United States' healthcare cost. Stem cell therapy represents a potential solution to fill the gap of limited organ donations at a decreased cost. Stem cell therapy also has potential use in cancer vaccine formulations. Human embryo-derived stem cells (ESC) exhibit a neoplastic propensity when terminally differentiated cell cultures contain any undifferentiated cells. Further, tissue derived from ESCs, when transplanted, have a risk of graft rejection from human leukocyte antigen (HLA) mismatch between donor and recipient. There have, thus, been efforts to develop alternative pluripotent stem cells that lack immunogenicity, tumorigenicity, and ethical controversies inherent with ESCs. Induced pluripotent stem cells (IPSCs) represent a source of pluripotent stem cells that could achieve these objectives.

To derive IPSCs historically, somatic cells were transfected with reprogramming molecules using retroviral delivery systems. However, retroviral transfection introduces exogenous DNA into the genome, disrupting genes, and thus increasing the risk of neoplastic effects and teratoma formation. Additionally, known retroviral methods require transfection of oncogenes c-Myc, L-Myc, and/or Lin-28. Lin28, c-Myc, and L-Myc are associated with several clinical malignancies and may increase the risk of neoplastic effects and teratoma formation long-term.

Episomal reprogramming is an ideal method for creating clinical-grade, safer, non-viral and integration-free IPSCs. Exogenous genes introduced through episomal vectors can be easily monitored through fluorescent tags such as Red Fluorescent Protein and their shut down can be easily detected. Unlike other methodologies, episomal vectors are only active on average for 17 to 21 days before reaching an undetectable level due to dilution and instability caused by cell division. However, episomal reprogramming has often been avoided since the reprogramming efficiency has been very low compared to other non-viral methods. To compensate for the lower reprogramming efficiency, episomal constructs comprising oncogenes such as c-Myc or a combination of L-Myc and Lin28 have been used. Even then, no IPSC colony formation was observed using an episomal reprogramming strategy that delivered the combination of Oct4, Sox2, Nanog, Lin28, c-Myc and Klf4. Only after the addition of a SV40 large T antigen gene to the combination of Oct4, Sox2, Nanog, Lin28, c-Myc and Klf4 genes could colony formation be observed with episomal delivery and, even then, the reprogramming efficiency was only approximately 0.0006 percent. However, SV40 large T antigen when introduced to cells can also immortalize them. SV40 large T antigen, when expressed, can also induce a malignant transformation, teratoma formation, and/or neoplasticity in a variety of cell lines. Others had avoided the use of SV40 large T antigen by adding NANOG, Lin28, and c-Myc with Oct-3/4 Klf4, and Sox-2, or by adding NANOG, Lin28, and L-Myc with Oct-3/4 Klf4, and Sox-2 and suppressing tumor checkpoint protein p53. Like SV40 large T antigen, Nanog is overexpressed in cancer cells. Mice which overexpress Nanog have hyperplastic outgrowths in the intestinal and colonic epithelium and the stratified epithelium of the caudal stomach and esophagus, and when co-expressed with Wnt-1, breast cancer tumors including metastasis. The additional requirements of oncogenes such as c-Myc, L-Myc, Lin-28, and Nanog represent a barrier to clinical use of the reprogrammed cells because the presence of the oncogenes in the reprogramming method, for however long, could increase the likelihood of a neoplastic event, teratoma formation, and cancer when the IPSCs or cells differentiated from IPSCs are transplanted into an organism.

There remains a need for alternative reprogramming methods and safer, more efficient methods for producing induced pluripotent stem cells from somatic cells.

SUMMARY OF THE INVENTION

Herein provided is a method for reprogramming a somatic cell comprising: (i) expressing exogenous Sox-2, Klf-4, and Oct3/4 in the somatic cell from DNA that has not integrated into genomic DNA of the somatic cell; inhibiting p53 activity in the somatic cell; and culturing the somatic cell in a reprogramming medium comprising an exogenous Alk-5 inhibitor, an exogenous histone deacetylase inhibitor, and an exogenous activator of glycolysis.

In an embodiment, the method for reprogramming a somatic cell, further comprises expressing exogenous EBNA-1 in the somatic cell from DNA that has not integrated into the genomic DNA of the somatic cell, and the DNA that has not integrated into the genomic DNA of the somatic cell comprises at least one plasmid with an Epstein-Barr virus origin of replication (oriP).

In an embodiment, also provided is such a method for reprograming a somatic cell, wherein one or more of L-Myc, c-Myc, Lin28, SV 40 large T antigen, and Nanog are not exogenously expressed.

In an embodiment, the method for reprogramming a somatic cell further comprises maintaining the cell in a dedifferentiation maintenance medium comprising basic fibroblast growth factor and transforming growth factor beta after being cultured in the reprogramming medium.

In an embodiment, the method for reprogramming a somatic cell involves a method as described above wherein the culturing which does not require feeder cells.

In an embodiment, the method for reprogramming a somatic cell has a reprogramming efficiency that exceeds 0.0006%.

In an embodiment, provided herein is a method for reprogramming a somatic cell, wherein inhibiting p53 activity in the somatic cell inhibits p53-induced cell cycle arrest or p53-induced apoptosis.

In an embodiment of the method for reprograming a somatic cell, inhibiting p53 activity in the somatic cell comprises suppressing p53 expression in the somatic cell.

In an embodiment of the method for reprograming a somatic cell, suppressing p53 expression comprises expressing antisense p53 RNA in the somatic cell from DNA that has not integrated into the genomic DNA of the somatic cell.

In an embodiment of the method for reprogramming a somatic cell, the Alk-5 inhibitor comprises 3-(6-Methyl-2-pyridinyl)-N-phenyl-4-(4-quinolinyl)-1H-pyrazole-1-carbothioamide (A83-01), the histone deacytylase inhibitor comprises sodium butyrate or valproic acid, and the activator of glycolysis comprises a phosphoinositide-dependent protein kinase-1 inhibitor selected from 5-(4-Chloro-phenyl)-3-phenyl-pent-2-enoic acid (PS48); α,α,-Dimethyl-4-[2-methyl-8-[2-(3-pyridinyl)ethynyl]-1H-imidazo[4,5-c]quinolin-1-yl]-benzeneacetonitrile (BAG956); N-[3-[[5-Iodo-4-[[3-[(2-thienylcarbonyl)amino]propyl]amino]-2-pyrimidinyl]amino]phenyl]-1-pyrrolidinecarboxamide (BX795); (3S,6R)-1-[6-(3-Amino-1H-indazol-6-yl)-2-(methylamino)-4-pyrimidinyl]-N-cyclohexyl-6-methyl-3-piperidinecarboxamide (GSK 2334470); 2-Amino-N-[4-[5-(2-phenanthrenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]phenyl]acetamide (OSU03012); and 4-Dodecyl-N-1,3,4-thiadiazol-2-yl-benzenesulfonamide (PHT427).

In an embodiment of the method for reprogramming a somatic cell, the somatic cell is an isolated cord blood or peripheral blood mononuclear cell, and the method further comprises pre-culturing the isolated cord blood or peripheral blood mononuclear cell in hematopoietic stem cell expansion media.

In an embodiment, the method for reprogramming a somatic cell yields an integration-free, virus-free, exogenous oncogene-free IPS cell.

Also provided herein is a method as described above in which the iPS cell is a human iPS cell.

Also provided herein is a method as described above wherein the iPS cell is differentiated into an endodermal, mesodermal, or ectodermal cell.

In an embodiment, also provided is a method for reprogramming a somatic cell comprising: expressing exogenous Sox-2, Klf-4, and Oct-3/4 in the somatic cell; suppressing p53 expression in the somatic cell; and culturing the somatic cell in a reprogramming medium comprising at least three different exogenous reprogramming-assistance factors to obtain an iPS cell free of exogenous oncogenes and exogenous viral elements.

In an embodiment, the method for reprogramming a somatic cell comprises expressing Sox-2, Klf-4, and Oct-3/4 in the somatic cell from episomal DNA.

In an embodiment, the method for reprogramming a somatic cell further comprises expressing EBNA-1 in the somatic cell and Sox-2, Klf-4, Oct-3/4, and EBNA-1 are expressed from at least one plasmid with an Epstein-Barr virus origin of replication (oriP).

Also described herein is a method for reprogramming a somatic cell as described above, wherein suppressing p53 expression in the somatic cell comprises expressing antisense p53 RNA in the somatic cell.

Herein also provided is a composition comprising a somatic cell and a cell culture medium, the somatic cell comprising episomal polynucleotides encoding EBNA-1, Sox-2, Klf-4, and Oct3/4, and the medium comprising an exogenous Alk-5 inhibitor, an exogenous histone deacetylase inhibitor, and an exogenous activator of glycolysis.

Herein also provided is a kit comprising (a) one or more non-integrating vectors encoding Sox-2, Klf-4, and Oct3/4; (b) an agent for inhibiting p53 activity; and (c) a reprogramming medium which comprises an Alk-5 inhibitor, a histone deacetylase inhibitor, and an activator of glycolysis.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

FIG. 1. Episomal vector design. A generalized vector map of an exemplary episomal vector based on the pCEP-4 episomal backbone containing an Epstein Barr virus origin of replication (OriP), SV40 poly-adenylation sequence, 2A cleavage sequence for tandem genes, a bacterial origin of replication, and ampicillin/hygromycin resistance genes is shown. As shown, each vector either contains a single gene or tandem genes separated by a 2A cleavage sequence.

FIG. 2. Exemplary combinations of vectors/reprogramming factors. FIG. 2 shows exemplary combinations of episomal vectors and reprogramming-assistance factors (PS48, A83-01, and sodium butyrate), used for somatic cell reprogramming. Combinations were categorized into those containing exogenous L-Myc and Lin28, those free of exogenous Myc (i.e., free of exogenous c-Myc and L-Myc) and Lin28, and those comprising exogenous c-Myc.

FIGS. 3A-3G. Exemplary Polynucleotide and Amino Acid Sequences For Use in Methods as Disclosed Herein. FIG. 3A shows: Red Fluorescent Protein (RFP) DNA sequence inserted into pCEP-4 for Vector N1 (SEQ ID NO.: 15), Red Fluorescent Protein (RFP) amino acid sequence as translated from Vector N1 (SEQ ID NO.: 16), Human l-Myc DNA sequence inserted into pCEP-4 for Vector N2 (SEQ ID NO.: 7), Human l-Myc amino acid sequence as translated from Vector N2 (SEQ ID NO.: 8), and Human Lin28 DNA sequence inserted into pCEP-4 for Vector N2 (SEQ ID NO.: 5). FIG. 3B shows: Human Lin28 amino acid sequence as translated from Vector N2 (SEQ ID NO.: 6), Epstein-Barr virus nuclear antigen 1 (EBNA-1) DNA sequence inserted into pCEP-4 for Vector N3 (SEQ ID NO.: 21), EBNA-1 sequence as translated from Vector N3 (SEQ ID NO.: 22), and Human c-Myc DNA sequence inserted into pCEP-4 for Vector N4 (SEQ ID NO.: 1). FIG. 3C shows: Human c-Myc amino acid sequence as translated from Vector N4 (SEQ ID NO.: 2), Human Sox-2 DNA sequence inserted into pCEP-4 for Vector N5 (SEQ ID NO.: 17), Human Sox-2 amino acid sequence as translated from Vector N5 (SEQ ID NO.: 18), Human Klf-4 DNA sequence inserted into pCEP-4 for Vector N5 (SEQ ID NO.: 3), and Human Klf-4 amino acid sequence as translated from Vector N5 (SEQ ID NO.:4). FIG. 3D shows: DNA sequence encoding antisense RNA for p53 mRNA inserted into pCEP-4 for Vector N6 (SEQ ID NO.: 12), Oct-3/4 DNA sequence inserted into pCEP-4 for Vector N7 (SEQ ID NO.: 9), and Oct-3/4 amino acid sequence as translated from Vector N7 (SEQ ID NO.: 10). FIG. 3E shows the nucleotides 1-5040 of the pCEP4 DNA sequence (SEQ ID NO.: 20). FIG. 3F shows nucleotides 5041-10186 of the pCEP4 DNA sequence (SEQ ID NO.: 20). FIG. 3G shows: DNA sequence for Epstein Barr virus origin of replication (OriP) in pCEP-4 and Vectors N1-7 (SEQ ID NO.: 11), DNA sequence for SV40 poly-adenylation sequence represented in pCEP-4 and Vectors N1-7 (SEQ ID NO.: 19), DNA sequence for p53 from mouse (SEQ ID NO.: 13), and Amino acid sequence for p53 from mouse (SEQ ID NO.: 14).

FIG. 4. Time sequence of IPSC reprogramming and cell expansion. FIG. 4 depicts the time line sequence of IPSC reprogramming and cell expansion.

FIGS. 5A-5D. Montage of Phase Contrast, Alkaline Phosphatase, Nanog, Oct4, Tra160. Montage of cultured human foreskin fibroblasts (HFFs) reprogrammed into IPSCs with episomal vectors free of Myc and Lin28 and IPSC reprogramming factors. Images were captured at day 14 of the IPSC reprogramming process. FIG. 5A shows typical IPSC colonies depicted by phase contrast microscopy. FIG. 5B shows representative IPSC colonies stained for alkaline phosphatase. FIG. 5C shows representative IPSC colonies exhibit pluripotency by immunofluorescent live stain for SSEA4. Each figure is representative of 4 separate experiments. Scale bar represents 100 microns. FIG. 5D shows representative IPSC colonies depicted by phase microscopy with corresponding pluripotent fluorescent biomarker of Nanog, Oct4 and TRA160 of the same colony. Scale bar represents 100 microns.

FIGS. 6A-6B. Ectopic episomal vectors are shut down in cultured IPSC colonies within 2 weeks in cells exposed to reprogramming-assistance factors and a mixture of episomal vectors free of Myc and Lin28. The figure shows the decrease in RFP episomal reporter protein expression in culture IPSC colonies at day 17. FIG. 6A: Black arrows point to iPSC colonies captured under phase microscopy. FIG. 6B: White arrows point to the corresponding RFP signal in the same colonies. As shown there is a complete loss of expression of RFP in the IPSC colonies demonstrating that episomal vectors are shut down within 2 weeks. The figure is representative of 4 separate experiments. Scale bar represents 100 microns.

FIGS. 7A-7B. Effect of reprogramming media, L-myc/Lin28, c-Myc, and oncogene free conditions on number of colonies. The number of IPSC colonies created in the presence and absence of IPSC reprogramming-assistance factors. FIG. 7A illustrates the numbers of colonies generated between the different vector constructs among cultured cells reprogrammed in the presence of reprogramming-assistance factors. Data are reported as the mean (±SE) number of colonies observed for cultured HFF reprogrammed with l-Myc/Lin28, c-Myc and in the absence of these oncogenes. Each test condition used 100,000 input cells. Each group represents a sample size of 4. FIG. 7B illustrates the number of colonies generated between the different vector constructs among cultured cells reprogrammed in the absence of reprogramming-assistance factors. Data are reported as the mean (±SE) number of colonies observed for cultured HFF reprogrammed with l-Myc/Lin28, c-Myc and in the absence of both oncogenes. Each group represented a sample size of 4. Data labeled with * show a statistical significant difference (p<0.05) between cultured cells treated with Myc and Lin28 and those cells treated without Myc and Lin28. NS denotes no significant difference.

FIG. 8. Effect of L-myc/Lin28, c-Myc, and oncogene free conditions on reprogramming efficiency. Impact of IPSC reprogramming-assistance factors in the presence and absence of Myc and Lin28. Reprogramming efficiency is expressed as the percentage of colonies counted per 100,000 of input cells×100. Data are reported as the mean (±SE). Each group represents a sample size of 4 replicates. Data labeled with * highlight a statistical significant difference (p<0.05) between cultured cells treated with Myc and Lin28 and those cells treated without Myc and Lin28. ** denotes a significant statistical difference (p<0.05) between cells transfected with c-Myc and l-Myc/Lin28.

FIG. 9. Effect of L-myc./Lin28, c-Myc, and oncogene free conditions on percent of colonies expressing SSEA4. IPSC reprogramming with reprogramming-assistance factors, PS48, A83-01, and sodium butyrate, exhibit the same percentage of pluripotent colonies in the presence and absence of Myc/Lin28. Figure depicts the percentage of colonies that express SSEA4 among cultured HFF exposed to l-Myc/Lin28, c-Myc and the absence of both oncogene groups. Data are reported as the mean (the standard error=0). All colonies stained positive for SSEA4. Each group represents a sample size of 4 replicates.

FIG. 10. HFF-Derived IPS Cells Converted to Cardiomyocytes Stained for Fluorescent Phalloidin (Green). Phalloidin binds to filamentous-actin, a protein component of heart muscle that together with tropomyosin and cardiac troponin executes a muscle contraction.

FIG. 11. HFF-Derived IPS Cells Converted to Cardiomyocytes Immunofluorescent for Cardiac Troponin (Green). Cardiac troponin is a protein that is found only in heart muscle.

FIG. 12. IPS Cells Converted to Mesoderm Immunofluorescent for Brachyury. Mesoderm is the middle layer of the gastrula and differentiates into tissues such as muscle, bone (except the jaw bone and ear bones), tubule cells of the kidney, and connective tissue including red blood cells. Brachury is a protein specifically expressed in the mesoderm.

FIG. 13. IPS Cells Converted to Neural Progenitor Cells Immunofluorescent for Nestin. Neural progenitor cells are derived from the ectoderm during neurulation, which is the first developmental event to give rise to a specific line of tissue, neural tissue. Neural Progenitor cells give rise to neurons and glia, through processes of neurogenesis and gliogenesis. Nestin is a neural progenitor cell marker, whose expression is largely lost after neurogenesis or gliogenesis.

FIG. 14. IPS Cells Converted to Neural Progenitor Cells Immunofluorescent for Paired box protein Pax-6. Neural progenitor cells are derived from the ectoderm during neurulation, which is the first developmental event to give rise to a specific line of tissue, neural tissue. Neural Progenitor cells give rise to neurons and glia, through processes of neurogenesis and gliogenesis. Pax-6 is a regulatory transcription factor important for brain development and is a neural progenitor cell marker, whose expression is largely lost after neurogenesis or gliogenesis.

FIG. 15. IPS Cells Converted to Endoderm Immunofluorescent for SRY-box 17 (Sox-17). Endoderm is the innermost layer of the gastrula and responsible for the origination of the alimentary canal, lung cells, endocrine glands, liver cells, and pancreatic cells. SRY-box 17 protein is a transcription factor regulating embryonic development of endodermal cells.

FIG. 16. IPS Cells Converted to Endoderm Immunofluorescent for Forkhead Box Protein A2 (FOXA2). Endoderm is the innermost layer of the gastrula and responsible for the origination of the alimentary canal, lung cells, endocrine glands, liver cells, and pancreatic cells. FOXA2 protein is a transcription factor regulating embryonic development of endodermal cells, particularly in the liver and pancreas.

FIG. 17. Time sequence of hematapoetic stem cell media exposure, IPSC reprogramming, and cell expansion of cultured cord blood-derived mononuclear cell (CBDMNC).

FIG. 18. Montage of cultured cord blood-derived mononuclear cell (CBDMNC) HSC cultured in differentiation media and then reprogrammed into IPSCs by transfecting with episomal vectors free of Myc and Lin28 and culturing in the presence of reprogramming media and IPSC reprogramming-assistance factors, PS48, A83-01, and sodium butyrate. Images were captured 22 days after transfection with episomal vectors. Typical IPSC colony depicted by phase contrast microscopy. Representative IPSC colony stained for alkaline phosphatase. Representative IPSC colony exhibited pluripotency by immunofluorescent live stain for SSEA4, Nanog, Oct4 and TRA160. Each figure is representative of 4 separate experiments. Scale bar represents 100 microns.

FIG. 19. Numbers of colonies generated from CBDMNCs transfected with 1) 1-Myc plus Lin28, 2) c-Myc, or 3) where l-Myc, Lin28, and c-Myc were omitted, then cultured in the presence and absence of HSC differentiation media. Each test condition used 1,000,000 input cells. (Mean±SEM number of colonies with a sample size of 4. Data labeled with “*” show a statistical significant difference (p<0.05) between cultured cells treated in the presence and absence of HSC differentiated media. Data labeled with “**” depicts a significant difference in colony formation between Myc and Lin28 and those cells treated without Myc and Lin28.)

FIGS. 20A-20C. CD34+ cells converted from CBDMNCs in the presence of HSC differentiation media as quantified by flow cytometry. Cultured CBDMNC were exposed to 7 days of HSC differentiation media and the amount of HSC differentiation was quantified by an antibody against human CD34+ cell expression. FIG. 20A shows a dot blot of CD34+ and CD34− cell populations. FIG. 20B shows frequency of CD34+ cells across log fluorescence when CBDMCs were exposed to HSC differentiation media-13% of CBDMNC differentiated into CD34+ cells after 7 days of exposure to HSC differentiation media. FIG. 20C shows frequency of CD34+ cells across log fluorescence when CBDMCs were not exposed to HSC differentiation media—a mere 1% of CBDMCs differentiated into CD34+ cells in the absence of HSC differentiation media.

FIG. 21. Number of IPSC Colonies Depend upon the Input Number of CBDMNCs, and transfection of c-Myc, l-Myc and Lin 28, or the absence of c-Myc, l-Myc, and Lin28. (Mean±SEM of number of colonies, n=4, ANOVA, and Tukey's HSD, *: p<0.05 compared to 100,000 input cells of the same vector construct. **: p<0.05 compared to 300,000 input cells of the same vector construct. ***: p<0.05 with transfection of Myc and/or Lin28 compared to the absence of Myc and Lin28 transfection at the same corresponding input cell number.)

FIG. 22. Reprogramming Efficiency depends upon whether L-Myc, c-Myc, or Lin28 were Transfected in Addition to Sox-2, Klf-4, Oct3/4 into cultured CBDMNC and not Input Cell Numbers. The number of input cells varied from 100,000; 300,000; 500,000; and 1,000,000 CBDMNCs. (Mean±SEM of reprogramming efficiency, ANOVA, Tukey's HSD, n=4, “*”: (p<0.05) compared to 100,000 input cells of the same vector construct; “*”: (p<0.05) compared to 300,000 input cells of the same vector construct; “***”: (p<0.05) in cultured cells transfected with exogenous Myc and Lin28 compared to cells not transfected with L-Myc, c-Myc, and Lin28 at each corresponding input cell number.)

FIG. 23. IPSC Colonies from CBDMNC Conversion with Reprogramming-assistance Factors, PS48, A83-01, and sodium butyrate, and HSC differentiation media are all Fully Reprogrammed Regardless in the Presence and Absence of Myc/Lin28. Figure depicts the percentage of colonies that express SSEA4 among cultured CBDMNC exposed to L-Myc/Lin28, c-Myc and the absence of both oncogene groups. Data are reported as the mean (the standard error=0). All colonies stained positive for SSEA4. Each group represents a sample size of 4 replicates. Full pluripotency was achieved at 300,000, 500,000 and 1,000,000 input cells.

FIG. 24. Montage of cultured IPSCs reprogrammed with peripheral blood MNC from a 57-year-old Caucasian female with alpha 1 antitrypsin deficiency with a PiZZ phenotype. Cells were reprogrammed into IPSC with episomal vectors free of Myc and Lin28 and HSC differentiation media. Images were captured at day 14 of the IPSC reprogramming process. Typical IPSC colony depicted by phase contrast microscopy. Representative IPSC colony stained positive for alkaline phosphatase. Representative IPSC colonies exhibited pluripotency by immunofluorescent live stain for SSEA4, Nanog, Oct4 and TRA160. Each figure is representative of 4 separate experiments. Scale bar represents 100 microns.

FIG. 25: Montage of cultured IPSCs reprogrammed from peripheral blood MNC among a 7-year-old Caucasian male with Cystic Fibrosis with the delta 508 mutation. Cells were reprogrammed into IPSC with episomal vectors free of Myc and Lin28 and HSC differentiation media. Images were captured at day 14 of the IPSC reprogramming process. Representative image of an entire culture stained with alkaline phosphatase. Representative IPSC colony stained for alkaline phosphatase. Representative IPSC colonies exhibited pluripotency by immunofluorescent live stain for SSEA4, Nanog, Oct4 and TRA160. Each figure is representative of 4 separate experiments. Scale bar represents 100 microns.

DETAILED DESCRIPTION OF THE INVENTION

The particulars shown herein are by way of example and for purposes of illustrative discussion of the various embodiments only and are presented in the cause of providing what is believed to be the most useful and readily understood description of the principles and conceptual aspects of the methods and compositions described herein. In this regard, no attempt is made to show more detail than is necessary for a fundamental understanding, the description making apparent to those skilled in the art how the several forms may be embodied in practice.

The present invention will now be described by reference to more detailed embodiments. This invention may, however, be embodied in different forms and should not be construed as limited to the embodiments set forth herein. Rather, these embodiments are provided so that this disclosure will be thorough and complete, and will fully convey the scope to those skilled in the art.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. The terminology used in the description herein is for describing particular embodiments only and is not intended to be limiting. As used in the description and the appended claims, the singular forms “a,” “an,” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. All publications, patent applications, patents, and other references mentioned herein are expressly incorporated by reference in their entirety.

Unless indicated to the contrary, the numerical parameters set forth in the following specification and attached claims are approximations that may vary depending upon the desired properties sought to be obtained and thus may be modified by the term “about”. At the very least, and not as an attempt to limit the application of the doctrine of equivalents to the scope of the claims, each numerical parameter should be construed in light of the number of significant digits and ordinary rounding approaches.

Notwithstanding that the numerical ranges and parameters setting forth the broad scope are approximations, the numerical values set forth in the specific examples are reported as precisely as possible. Any numerical value, however, inherently contains certain errors necessarily resulting from the standard deviation found in their respective testing measurements. Every numerical range given throughout this specification will include every narrower numerical range that falls within such broader numerical range, as if such narrower numerical ranges were all expressly written herein.

Advantages and Features

As described above, provided herein are methods for reprogramming a somatic cell comprising expressing exogenous Sox-2, Klf-4, and Oct3/4 in the somatic cell from DNA that has not integrated into genomic DNA of the somatic cell; inhibiting p53 activity in the somatic cell; and culturing the somatic cell in a reprogramming medium comprising, for example, an exogenous Alk-5 inhibitor, an exogenous histone deactylase inhibitor, and an exogenous activator of glycolysis. Methods for reprogramming a somatic cell as described herein do not require introduction of DNA that has integrated into the genomic DNA of the somatic cell insofar as the introduced DNA comprises at least one plasmid with an Epstein-Barr virus origin of replication (oriP). Another advantage is that methods for reprograming a somatic cell as described herein need not involve exogenously expressing one or more of Nanog, L-Myc, c-Myc, Lin28, and SV40 large T-antigen. Reprogramming may be further accomplished by maintaining the cell in a dedifferentiation maintenance medium, also known as an IPSC growth medium, comprising basic fibroblast growth factor and transforming growth factor beta after being cultured in the reprogramming medium.

Other features and advantages will be evident to those of skill in the art. For example, a method for reprogramming a somatic cell as described herein may include inhibiting p53 activity in the somatic cell to further inhibit p53-induced cell cycle arrest or p53-induced apoptosis. Methods as described herein also do not require feeder cells during culturing and may achieve reprogramming efficiencies that equal or exceed 0.0006%.

Methods for reprogramming a somatic cell as described herein further have the advantage that they may be applied to both adherent and non-adherent cells. When performed with a non-adherent cell, such as isolated cord blood or peripheral blood mononuclear cell, the method may comprise a pre-culturing step that comprises isolating the cord blood or peripheral blood mononuclear cell in hematopoietic stem cell expansion media.

The skilled artisan will further appreciate that methods for reprogramming a somatic cell as described herein may yield an integration-free, virus-free, exogenous oncogene-free iPS cell.

Initial Isolation of Cells, Initial Culturing Are not Particularly Limited.

Somatic cells may be initially isolated and cultured to provide a starting material. The somatic cell is not particularly limited but it should preferably be isolated from a cell known to carry the full-genetic repertoire of the organism, such as a diploid cell, and should not be isolated from cells predisposed to having some or all of the genetic repertoire eliminated, such as cells from the gonads, red blood cells, and platelets. Cells with multiple nucleuses are not particularly preferred either, such as skeletal muscle cells, and some forms of white blood cells. Somatic cells can include adhesive and non-adhesive cells, cells of endodermal, ectodermal, or mesodermal origin. Somatic cells can include fibroblasts, endothelial cells, epidermal cells, lymphocytes, neurons, ependymal cells, oligodendrocytes, Schwann cells, astrocytes, glia, enterocytes, goblet cells, Paneth cells, parietal cells, pitt cells, gastric cells, chymogenic cells, enteroendocrine cells, alpha cells, beta cells, keratinocytes, submucosa cells, stromal cells, tenocytes, adipocytes, mast cells, macrophages, epithelial cells, basal cells, squamous epithelial cells, ondotoblasts, endodontium cells, osteoclasts, osteoblasts, myeloblasts, basophils, neutrophils, eosinophils, monocytes, plasma cells, B lymphocytes, T lymphocytes, natural killer cells, small lymphocytes, myelocytes, normoblasts, and myeloplaxe. In the event a progenitor cell is used, such as a common myeloid progenitor cell, a common lymphoid progenitor cell, or a neural progenitor cell, it may be necessary to differentiate the cell by exposing the cell in culture to differentiation factors before the reprogramming the somatic cell.

Generation of DNA that does not Integrate into the Genome Transfection

To reprogram the somatic cells, the cells may express Sox-2, Klf-4, and Oct3/4 proteins, and, preferably, Epstein-Barr nuclear antigen-1 (EBNA-1) protein from exogenous genetic material that has not integrated into the genome of the somatic cell. The proteins may be expressed at levels higher than those observed in a cell which has not been manipulated to express exogenous Sox-2, Klf-4, and Oct3/4 proteins but otherwise has undergone all the other treatments, such as suppression of p53 activity and growth in media containing reprogramming-assistance factors. The exogenous genetic material that has not integrated into the genome of the somatic cell includes, but is not limited to, DNA that has not integrated into the genome of the somatic cell, and such DNA can include, but is not limited to plasmids. Preferably, the plasmids include an Epstein-Barr virus origin of replication (oriP) and/or a gene for EBNA-1 expression to further ensure that the plasmids do not integrate into the genome of the somatic cell. It is contemplated that Sox-2, Klf-4, Oct3/4, and optionally EBNA-1 and optionally other gene sequences coding for protein can be expressed on separate plasmids or DNA molecule or on the same plasmid or DNA molecule. Whether Sox-2, Klf-4, Oct3/4, and optionally EBNA-1, and optionally other gene sequences coding for protein are all expressed on one plasmid or DNA molecule, each individually on a separate plasmid or DNA molecule, or in some combination of two or more plasmids or DNA molecule (e.g. Klf-4 and Oct3/4 on the same plasmid, and Sox-2 and EBNA-1 on distinct plasmids or DNA molecule) depends upon the length of each protein coding sequence, the length of the overall plasmid or DNA molecule, and the method of transfection. For example, certain virion vectors for transfection can range from 4.7 to 8.7 kilo base pairs for AAV vectors, whereas herpes virus sequence can be 150 kilo base pairs. Likewise the optimal plasmid or DNA molecule lengths can vary from across non-viral vector methods of transfection such as nucleofection or lipofection protocols.

One particular embodiment of expressing exogenous Sox-2, Klf-4, Oct3/4 and optionally EBNA-1, can be through the transfection of one or more of plasmids, which contain the gene sequences for Sox-2 represented by SEQ ID NO: 17, Klf-4 represented by SEQ ID NO: 3, Oct3/4 represented by SEQ ID NO: 9, and optionally EBNA-1 represented by SEQ ID NO:21. In such an embodiment, the transfected somatic cell will express a Klf-4 protein of SEQ ID NO: 4, an Oct3/4 protein of SEQ ID NO: 10, a Sox-2 protein of SEQ ID NO: 18, and optionally an EBNA-1 protein of SEQ ID NO: 22_from the transfected incorporated plasmid. In one particular embodiment, the genes encoding for Sox-2, Klf-4, Oct-3/4, and EBNA-1 are incorporated into the pCEP-4 plasmid of SEQ ID NO: 20. In another particular embodiment, c-Myc, SEQ ID NO: 1 may be incorporated in the pCEP-4 plasmid of SEQ ID NO: 20 and the incorporated plasmid then may be transfected into the somatic cell. In such an embodiment, the transfected somatic cell will express c-Myc protein of SEQ ID NO: 2 from the transfected incorporated plasmid. In another particular embodiment, a Lin28 of SEQ ID NO: 5, and l-Myc of SEQ ID NO: 7_may be incorporated in the pCEP-4 plasmid of SEQ ID NO: 20 and the incorporated plasmid may be then transfected into the somatic cell. In such an embodiment, the transfected somatic cell will express proteins of SEQ ID NO: 6, and SEQ ID NO: 8, respectively, from the transfected incorporated plasmid.

In an embodiment, an exemplary Sox-2 amino acid sequence may be an amino acid sequence which has at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the Sox-2 amino acid sequence transcribed and translated from the somatic cell genome, and which is capable of functioning as a transcription factor within the cell. In an embodiment, an exemplary Sox-2 nucleotide sequence may be a nucleotide sequence which has at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the Sox-2 nucleotide sequence of the somatic cell and which is capable of being transcribed and translated into a Sox-2 protein which is capable of functioning as a transcription factor within the cell.

In an embodiment, an exemplary Klf-4 amino acid sequence may be an amino acid sequence which has at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the Klf-4 amino acid sequence transcribed and translated from the somatic cell genome, and which is capable of functioning as a transcription factor within the cell. In an embodiment, an exemplary Klf-4 nucleotide sequence may be a nucleotide sequence which has at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the Klf-4 nucleotide sequence of the somatic cell and which is capable of being transcribed and translated into a Klf-4 protein which is capable of functioning as a transcription factor within the cell.

In an embodiment, an exemplary Oct3/4 amino acid sequence may be an amino acid sequence which has at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the Oct-3/4 amino acid sequence transcribed and translated from the somatic cell genome, and which is capable of functioning as a transcription factor within the cell. In an embodiment, an exemplary Oct-3/4 nucleotide sequence may be a nucleotide sequence which has at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the Oct-3/4 nucleotide sequence of the somatic cell and which is capable of being transcribed and translated into a Oct-3/4 protein which is capable of functioning as a transcription factor within the cell.

In an embodiment, an exemplary EBNA-1 amino acid sequence may be an amino acid sequence which has at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the EBNA-1 as disclosed herein, and which is capable of maintaining episomal vector replication. In an embodiment, an exemplary EBNA-1 nucleotide sequence may be a nucleotide sequence which has at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the EBNA-1 nucleotide sequence as disclosed herein and which is capable of being transcribed and translated into a EBNA-1 protein which is capable of functioning in episomal DNA maintenance during reprogramming.

It is further contemplated that the Oct3/4, Klf-4, and Sox-2 sequences of protein or nucleotides encoding protein can vary from species to species, and within species, and that the nucleotide and amino acid sequences are not limited to a particular sequence identified at the time of filing this application. It is further contemplated that the EBNA-1 sequences of protein or nucleotides encoding protein can vary from varieties of cytomegaloviruses, and that the nucleotide and amino acid sequences are not limited to a particular sequence explicitly disclosed herein. For example, Oct3/4, Klf-4, and Sox-2 polymorphisms identified in the human population, rat population, mouse population, or the population of other species are included herein. It is further preferred that when transfecting a somatic cell with DNA encoding for exogenous DNA, that the sequences of Oct3/4, Klf-4, and Sox-2 be selected from sequences identified from the same species as the somatic cell. It is further preferred that when transfecting a somatic cell with DNA encoding for exogenous Oct3/4, Klf-4, and Sox-2, that the sequences of Oct3/4, Klf-4, and Sox-2 be the same as that of the genome of somatic cell.

It is further contemplated that c-Myc, L-Myc, and/or Lin28 are also expressed from exogenous genetic material that has not integrated into the genome of the somatic cell. In some embodiments, L-Myc and Lin28 are co-expressed. It is preferred that the c-Myc, L-Myc, and/or Lin28 are expressed at levels higher than those observed in a cell which has not been manipulated to express exogenous c-Myc, L-Myc, and/or Lin28 proteins but otherwise has undergone all the other treatments, such as suppression of p53 activity and growth in media containing reprogramming-assistance factors.

It is further preferred that the somatic cell not be transfected to express exogenous SV 40 large T antigen.

Exogenous transfection may omit transfection of DNA encoding SV40 large T antigen and Nanog that does not integrate into the host cells' genome. It is further preferred that the exogenous transfection omit transfection of exogenous DNA that does not integrate into the host cell's genome and encodes c-Myc along with SV40 large T antigen and Nanog. It is further preferred that the exogenous transfection omit transfection of exogenous DNA that does not integrate into the host cell's genome and encodes L-Myc along with SV40 large T antigen and Nanog. It is further preferred that the exogenous transfection omit transfection of exogenous DNA that does not integrate into the host cell's genome and encodes Lin-28 along with SV40 large T antigen and Nanog. It is further preferred that the exogenous transfection omit transfection of exogenous DNA that does not integrate into the host cells' genome and encodes L-Myc and Lin-28 along with SV40 large T antigen and Nanog. It is further preferred that the exogenous transfection omit transfection of exogenous DNA that does not integrate into the host cells genome and encodes c-Myc, L-Myc and Lin-28 along with SV40 large T antigen and Nanog.

It is further contemplated that the expression is transient for the exogenous genes that have not integrated into the genome particularly when the genes are located within a plasmid with an OriP origin of replication, for example, as represented by SEQ ID NO: 11. Transient transfection may also be achieved by use of an inducible promoter, such as chemically-regulated promoters such as those regulated by the presence or absence of alcohol, tetracycline, steroids, or a metal; and physically-regulated promoters such as those regulated by the presence or absence of light or low or high temperatures. It is further contemplated that the expression of Oct-3/4, Klf-4, Sox-2, EBNA-1 c-Myc, l-Myc, and/or Lin28 is/are transient. It is further contemplated that the transient expression of the exogenous genes that have not integrated into the genome, such as but not limited to Oct-3/4, Klf-4, Sox-2, EBNA-1 c-Myc, l-Myc, and/or Lin28, lasts for 3-weeks, 17-days, or 2-weeks after the last transfection, if multiple transfections are attempted. It is further contemplated that the expression of the exogenous genes that have not integrated into the genome, such as but not limited to Oct-3/4, Klf-4, Sox-2, EBNA-1 c-Myc, l-Myc, and/or Lin28, ceases after 3-weeks, 17-days, or 2-weeks after the last transfection, if multiple transfections are attempted. It is preferred that the expression ceases after 3-weeks. It is further preferred that the expression ceases after 17-days. It is further preferred that the expression ceases after 2-weeks. It is further preferred that the length of transient expression inversely correlate with the number of genes encoding for EBNA-1 that are transfected into the somatic cell.

Confirmation of Transfection of DNA that does not Integrate into the Genome is not Particularly Limited

It is further contemplated that the plasmids contain genetic elements which can serve as markers for confirming that the plasmid has been transfected into the somatic cell. Such genetic elements which can serve as markers confirming transfection of the plasmid include, but are not limited to, incorporation of genes encoding for GFP, YFP, RFP, mCherry, dTomato, DsRed, Crimson, and other fluorescent proteins which may be expressed by the somatic cell after transfection. Non-fluorescent markers that confirm transfection of a plasmid are also contemplated. In one embodiment, the DNA sequence encoding for RFP, such as SEQ ID NO: 15, may be incorporated into the pCEP-4 plasmid of SEQ ID NO: 20, and the incorporated plasmid may be transfected into the somatic cell. In such an embodiment, the somatic cell may express the RFP protein of SEQ ID NO: 16 from the transfected incorporated plasmid.

Additionally, transfection can be confirmed by measuring expression of mRNA or protein for Sox-2, Klf-4, Oct-3/4 and/or EBNA-1. Additionally qPCR measurement of sequences in the plasmid can evaluate efficiency of transfection. The means of confirming transfection are thus not particularly limited.

The amount of plasmid transfected, in sum or for each individual plasmid, is not particularly limited. Several different amounts of plasmid may be tested and the amount of plasmid that results in the most or a substantial number of cells expressing the selected marker, such as RFP, may be used. In this instance, a substantial number of cells refers to the number of cells within one standard deviation of the maximal number of cells transfected and wherein the number of replicates within each condition is 6. The amount of plasmid may be either the total amount of all the plasmids, if Sox-2, Klf-4, Oct-3/4 and/or EBNA-1 are contained on two or more plasmids. The amount of plasmid transfected can be 0.5 μg, 1 μg, 2 μg, 3 μg, 4 μg, 5 μg, 6 μg, 7 μg, 8 μg, or 9 μg per 100,000 cells being transfected, as well as fractions in between, such as 2.3 μg, 3.5 μg, 4.7 μg. Thus, the amount of plasmid transfected may be any amount from 0.1 to 10 μg per 100,000 cells. The timing of testing for and visualising the marker for transfection in part depends upon the promoter controlling the expression. Some promoters will express the downstream protein coding sequence after 7 days, such as chicken ovalbumin upstream promoter transcription factor. Others such as cytomegalovirus promoter (pCMV), can be express the downstream protein coding sequence within 48 hours. The timing of expression may also depend upon the transfection method including the viral vectors used.

Suppression of p53 Activity is not Particularly Limited

The suppression of p53 activity is not particularly limited in the means by which it is achieved. Activity of p53 may be suppressed by the following manipulations to the cell: administration of pharmacological inhibitors, reduction of p53 protein expression, or by introduction of an interfering protein that competes with or interacts with p53 to suppress its activity. One such inhibitor of p53 activity is mdm2, which interacts with and suppresses p53 activity until cellular injury such as DNA damage, cell cycle abnormalities or hypoxia, trigger the dissociation of mdm2 and p53. Therefore, it is contemplated, and is not limited to, the introduction of modified mdm2 or mdm2-mimetics that do not dissociate from endogenous p53 protein in response to cellular injury.

Reduction of p53 protein expression can further be achieved by reducing the expression of p53 mRNA or by suppression of p53 gene transcription. Genetic modifications such as gene deletion, insertion of stop codons, or introductions of single nucleotide polymorphisms into the p53 gene in the genome can result in a p53 protein with reduced activity, when the modified gene is transcribed and translated. However, these methods are not preferred as they may permanently modify the activity of a tumor suppressor protein in the reprogrammed cells and any cells that differentiate from the reprogrammed cells into somatic cells again. Pharmacological inhibition and knock-down approaches are preferred.

Pharmacological Inhibition of p53

Pharmacological inhibitors of p53 include, but are not limited to, pifithrin-α, cyclic pifithrin-α, pifithrin-μ, RITA, SJ 172550, and/or nutlin-3, and pharmaceutically acceptable salts thereof, such as pifithrin-α hydrobromide. Knock-down approaches include, but are not limited to, administration of antisense oligonucleotides, siRNA, RNAi, transfection of genes encoding for antisense oligonucleotides, siRNA, RNAi, all of which can be administered with or without the assistance of virion vectors, nucleofection, electroporation, or lipofectamine transfection reagents to promote cellular uptake of the nucleic acids.

Knockdown Approaches for Suppressing p53 Activity

Antisense oligonucleotides include antisense oligonucleotides modified to resist cellular and extracellular degradation such as locked nucleic acids (LNAs). With LNAs the 2″-hydroxyl group is linked to the 3′ or 4° carbon atom of the sugar ring thereby forming a bicyclic sugar moiety, and is preferably a methelyne (—CH₂—)_(n) group bridging the T oxygen atom and the 3′ or 4′ carbon atom wherein n is 1 or 2. Other modifications of antisense oligonucleotides to resist cellular and extracellular degradation include 2′-allyl (2′-CH₂-CH═CH₂), T-aminopropoxy (2′-OCH₂CH₂CH₂NH₂), 2′-O-allyl (2′-O—CH₂—CH═CH₂), 2′-methoxy (2′-O—CH₃), and 2′-fluoro (2′-F). Other modifications to the antisense oligonucleotides include modifications at the 3′ position of the sugar on the 3′ terminal nucleotide or to the 5′ position of 5′ terminal nucleotide, or incorporation of 2°-5′ linked oligonucleotides. Antisense oligonucleotides that resist cellular and extracellular degradations may also be achieved by replacing pentofuranosyl sugar with sugar mimetics such as cyclobutyl moieties.

Antisense oligonucleotides can also be generated in the cell, such as in Example 1 below and FIG. 1. In Example 1 and FIG. 1, SEQ ID NO: 12 is a DNA sequence encoding antisense RNA for p53 mRNA. The SEQ ID NO: 12 DNA sequence encoding antisense RNA for p53 mRNA may be incorporated into the pCEP-4 vector construct, SEQ ID NO: 20. Thereafter, the incorporated construct of pCEP-4 and DNA sequence encoding antisense RNA for p53 mRNA may be transfected into the cell, for example, the cell of Example 1 below. The introduction of a gene encoding for antisense for p53 is not particularly limited such that it can include a number of different promoters, transcription initiators, and gene sequences to effect p53 protein knockdown. It is particularly preferred that the antisense sequence be directed to and complementary with the sequence of p53 mRNA that is near the initiation sequence for p53 translation.

Means of Confirming that p53 Activity is Suppressed is not Particularly Limited.

Suppression of p53 activity may include partial reduction of p53 activity within a cell as well as complete reduction of p53 activity within the cell. To determine whether a cell has suppressed p53 activity may be determined by comparing p53 activity in the cell to be reprogrammed against the same cell in which p53 activity is unmanipulated but which has otherwise has undergone all the other treatments contemplated, such as induction of exogenous Sox-2, Klf-4, Oct-3/4 and growth in media containing reprogramming-assistance factors (hereafter p53-unmanipulated cells). The p53-unmanipulated cell may be exposed to a scrambled oligonucleotide that is not complementary to any mRNA sequence of the cell, and the exposure to the scrambled oligonucleotide may be through the same means as with the manipulated cell, whether this be exposure to the scrambled oligonucleotide directly or transfection of a vector that expresses the scrambled oligonucleotide. The percentage of decrease in p53 protein which suppresses p53 activity can vary according to the knockdown approach, such as antisense oligonucleotides, siRNA, and RNAi. For example, a 5%, 10%, or 15% reduction in p53 protein in cells treated with an antisense oligonucleotide to p53 mRNA or transfected with a vector encoding for antisense oligonucleotides to p53 mRNA compared to p53-unmanipulated cells, can suffice to induce a physiologically effective reduction in p53 protein activity sufficient to reprogram somatic cells. In such cases, the antibody used by western blot to detect p53 protein may be generated using an antigen sequence from the p53 protein from the same species or a different species against which the anti-sense sequence was generated. For example, if sufficient homology exists for p53 across mouse and human, a p53 protein sequence from mouse, represented by SEQ ID NO: 14, and encoded for by the mouse p53 gene represented by SEQ ID NO: 13 can be used to select an antigen sequence against which an antibody is generated in a third species. The anti-p53 antibody derived from the mouse p53 protein sequence represented by SEQ ID NO: 14 can be tested on human p53 protein to determine whether the antibody cross reacts with human p53 antibody in a specific manner without cross reacting with other human proteins. As another example, siRNA or RNAi approaches may achieve a 30%, 40%, or 50% reduction in p53 protein in the cells treated with siRNA or RNAi compared to p53-unmanipulated cells in order to observe physiologically effective reduction in p53 protein activity sufficient to reprogram somatic cells.

Whether p53 activity is sufficiently suppressed by the manipulation to suppress p53 activity in the somatic cell, such as through a knock-down approach or pharmacological inhibition, may be determined by measuring the reprogramming efficiency. For example, a higher reprogramming efficiency may suggest that p53 activity was suppressed. In this regard, a reprogramming efficiency of 0.0006% may be used as a marker for determining whether the method of suppressing p53 activity was effective. Alternatively, other proxies may be used for determining whether the manipulation suppressed p53 activity; these include but are not limited to measuring cellular transduction pathways downstream of p53. For example, p53, when activated, can in turn trigger cell cycle arrest, leading to DNA repair and then a restart of the cell cycle. Alternatively, p53 can trigger apoptosis, DNA cleavage, and death and elimination of damaged cells, when activated. To determine whether the manipulation, such as a knock-down approach or pharmacological inhibition, suppresses p53 activity, somatic cells may be: 1) stained for cell cycle markers to determine whether the cell cycle has been arrested, 2) observed for markers for DNA repair, 3) observed for markers for apoptosis, and/or 4) observed for activation of miR-34a and miR-145, and then the manipulated cells can be compared against the same markers in p53-unmanipulated cells. Several markers including markers for apoptosis and markers for cell cycle arrest may be measured with the same manipulation and compared against p53-unmanipulated cells. When p53 is suppressed by the manipulation, both apoptosis and cell cycle arrest may be suppressed relative to p53-unmanipulated cells; however, it is also contemplated that only cell cycle arrest or only apoptosis is suppressed in response to p53 suppression when compared to p53-unmanipulated cells. The staining for apoptosis and cell cycle arrest are not particularly limited and commercially available methods are readily available. For example, markers for apoptosis can include TUNEL staining, caspase-3 staining, bcl-2 staining, surviving staining, ubiquitin staining, markers for DNA damage, or markers for cell membrane “blebbing,” each of which can be measured by counting the number of cells reaching a threshold amount of staining for the marker or quantifying the overall number of stains. Cell cycle arrest may be measured by staining for markers of G1, S, G2, and M phases, and the number of cells in each phase can be counted. An increase in the number of cells in the G1 or G2 in the p53-manipulated condition compared to the p53-unmanipulated condition can indicate that p53 activity has been suppressed.

Culturing with Reprogramming-assistance factors.

Cells may be exposed to reprogramming-assistance factors present in the culturing media. Reprogramming-assistance factors are discrete from Sox-2, Klf-4, Oct-3/4, EBNA-1, and exogenously expressed oncogenes such as c-Myc, l-Myc, Lin28, Nanog, and SV40 large T antigen.

The term “reprogramming-assistance factor” as used herein refers to an extracellular molecule that modulates the epigenetic programming, the state of differentiation, and/or the metabolism of a cell and assists in the reprogramming of a somatic cell expressing episomal Sox-2, Klf-4, and Oct-3/4.

For example, a molecule that may modulate epigenetic programming may be a molecule that inhibits or activates an intracellular enzyme that modifies DNA or modifies proteins that bind to DNA. One such intracellular enzyme that modifies DNA is DNA methyltransferase, which methylates DNA; another is ten eleven translocation enzyme (TET) which, in part, reverses DNA methylation. An intracellular enzyme that could modify a protein associated with DNA is histone deacetylase (HDAC), which removes acetyl groups from histones, or histone acetyltransferase, which adds acetyl groups to histones, or histone methyltransferase which adds methyl groups to histones, or histone demethylases, which removes methyl groups from histones. Thus, inhibitors and activators of HDAC, DNMT, TET, histone acetyltransferases, histone demethylases, and histone methyltransferases are contemplated as reprogramming-assistance factors.

A molecule that may modify the state of differentiation of a cell is a molecule that can modulate developmental growth factors important for the maintenance of stem cells or the differentiation of stem cells into somatic cells. For example, beta-catenin, transforming growth factor-beta, glycogen-synthase kinase-3 β (GSK-313), and alk5 are considered part of the Wnt signaling pathway. Wnt signaling, through beta-catenin, transforming growth factor-beta, glycogen-synthase kinase-3, and/or alk5, has been shown to be important for gastrulation, the differentiation of neural crest cells into the bones of the jaw and inner ear, for stem cell renewal, for epithelial to mesenchymal transitions, and for differentiation of cells into mesodermal lineages. In some cases, the Wnt pathway can involve a signaling cascade where one protein activates another protein. In some cases, the Wnt pathway can involve a signaling cascade where one protein inhibits another protein. In some cases, the Wnt pathway can involve a signaling cascade where one protein inhibits a second protein, and the second protein inhibits a third protein (wherein the Wnt pathway when activated involves the disinhibition of the third protein). A molecule that can modulate the state of differentiation of a cell or developmental growth factors important for the maintenance of stem cells or the differentiation of stem cells into somatic cells, can thus activate or inhibit the developmental growth factor signaling cascade. For example, it may be beneficial to inhibit alk5, but if alk5 signaling inhibits another protein in the pathway such as GSK-3β, which in turn phosphorylates beta-catenin, then it may be beneficial to use an GSK-3β activator instead of an Alk-5 inhibitor to achieve the same result of reducing beta-catenin phosphorylation and increase beta-catenin mediated transcription of Wnt-responsive genes. Thus a small or large molecule which modulates a state of differentiation may be either an activator or an inhibitor of growth factor signaling cascade molecules, including Wnt1 signaling cascade members. Other molecules and signaling pathways are also important for the differentiation of other cells into lineages of ectodermal, mesodermal, and endodermal origins.

A molecule that may modulate the metabolism of the cell, may be a molecule with modulates the glycolysis of the cell. Phosphoinositide-dependent protein kinase-1 is known to modulate the glycolysis of the cell and therefore an inhibitor phosphoinositide-dependent protein kinase-1 is also known to modulate glycolysis of the cell.

The exposure to reprogramming-assistance factors may occur before, concurrent with or after suppression of p53 activity or may occur before, concurrently with, or after transfection of and expression of exogenous Sox-2, Klf-4, and/or Oct-3/4. The culturing conditions for providing reprogramming-assistance factors are not particularly limited. In some embodiments, the reprogramming-assistance factors may be placed into the reprogramming media and the reprogramming media may be placed on the somatic cells which have been transfected with Sox-2, Klf-4 and Oct-3/4, or in which Sox-2, Klf-4 and Oct-3/4 have been, or are in the process of being, or are going to be exogenously expressed from DNA that has not integrated into the genome. In some embodiments, the reprogramming media may be comprised of a base media which is further comprised of 50% Dulbecco's Modified Eagle's Medium (DMEM) and 50% Ham's F-12 Media (50% DMEM/50% Ham's F-12 being also known as DMEM/F-12). In some embodiments, the reprogramming media is an admixture of the DMEM/F12 media and 1×N-2 Supplement. In some embodiments, the reprogramming media is an admixture of the DMEM/F12 media and 1×B-27 Supplement. In some embodiments, the reprogramming media is an admixture of the DMEM/F12 media and 1×MEM non-essential amino acids. In some embodiments, the reprogramming media is an admixture of the DMEM/F12 media and 1× Glutamax Supplement. In some embodiments, the reprogramming media is an admixture of the DMEM/F12 media and 1 mM glutamine supplement. In some embodiments, the reprogramming media is an admixture of the 1×DMEM/F12 with HEPES (ThermoFisher Scientific, Waltham, Mass.), 1×N-2 Supplement (ThermoFisher Scientific, Waltham, Mass.), 1×B-27 Supplement (ThermoFisher Scientific, Waltham, Mass.), 1×MEM Non-Essential Amino Acids (ThermoFisher Scientific, Waltham, Mass.) 1× Glutamax (ThermoFisher Scientific, Waltham, Mass.) and 1× Beta-Mercaptoethanol (ThermoFisher Scientific, Waltham, Mass.).

In some embodiments, the reprogramming-assistance factors may include at least one HDAC inhibitor. In some embodiments the HDAC inhibitor may be sodium butyrate or valproic acid.

In some embodiments, the reprogramming-assistance factors may include at least one Alk-5 inhibitor. In some embodiments, the Alk-5 inhibitor may be 3-(6-Methyl-2-pyridinyl)-N-phenyl-4-(4-quinolinyl)-1H-pyrazole-1-carbothioamide (A83-01), 4-[4-(1,3-benzodioxol-5-yl)-5-(2-pyridinyl)-1H-imidazol-2-yl]benzamide, 4-[4-[3-(2-Pyridinyl)-1H-pyrazol-4-yl]-2-pyridinyl]-N-(tetrahydro-2H-pyran-4-yl)-benzamide, or 6-[2-(1,1-Dimethylethyl)-5-(6-methyl-2-pyridinyl)-1H-imidazol-4-yl]quinoxaline.

In some embodiments, the reprogramming-assistance factors may include at least one activator of glycolysis. In some embodiments, the activator of glycolysis includes at least one phosphoinositide-dependent protein kinase-1 inhibitor. In some embodiments, the phosphoinositide-dependent protein kinase-1 inhibitor(s) may include at least one of 5-(4-Chloro-phenyl)-3-phenyl-pent-2-enoic acid (PS48); α,α,-Dimethyl-4-[2-methyl-8-[2-(3-pyridinyl)ethynyl]-1H-imidazo[4,5-c]quinolin-1-yl]-benzeneacetonitrile (BAG956); N-[3-[[5-Iodo-4-[[3-[(2-thienylcarbonyl)amino]propyl]amino]-2-pyrimidinyl]amino]phenyl]-1-pyrrolidinecarboxamide (BX795); (3S,6R)-1-[6-(3-Amino-1H-indazol-6-yl)-2-(methylamino)-4-pyrimidinyl]-N-cyclohexyl-6-methyl-3-piperidinecarboxamide (GSK 2334470); 2-Amino-N44-[5-(2-phenanthrenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]phenyllacetamide (OSU03012); and 4-Dodecyl-N-1,3,4-thiadiazol-2-yl-benzenesulfonamide (PHT427).

In some embodiments, the reprogramming-assistance factors may include sodium butyrate, A83-01, and PS48. In some embodiments, the reprogramming-assistance factors may include sodium butyrate, A83-01, PS48, Fibroblast Growth Factor-2 (also known as basic-Fibroblast Growth Factor, FGF-2), and Transforming Growth Factor-13 (TGF-β). FGF-2 is considered important for maintaining the IPSCs, once reprogrammed, in a de-differentiated state and is not considered necessary for the reprogramming process or survival of the reprogrammed cells. Likewise, TGF-β is not considered necessary for the reprogramming or the survival of the reprogrammed cells but is instead important for low level intracellular signaling through Alk-5, and/or the Transforming Growth Factor-13 receptor 2, via their inhibition or activation of SMAD2/3, SMAD4, Takl, MKK3/6, MKK4, glycogen synthase kinase-3, and/or beta-catenin pathways to maintain IPSCs, once reprogrammed, in a de-differentiated state.

In some embodiments, FGF-2 and TGF-β are added with the first administration of the other reprogramming-assistance factors, such as the Alk5 inhibitor, HDAC inhibitor, and phosphoinositide-dependent protein kinase-1 inhibitor. In some embodiments, FGF-2 and TGF-β are added with the subsequent administration of the other reprogramming-assistance factor, such as the A1k5 inhibitor, HDAC inhibitor, and phosphoinositide-dependent protein kinase-1 inhibitor, but not the first administration of the other reprogramming-assistance factors. In some embodiments, FGF-2 and TGF-β are added after the administration of and removal of the other reprogramming-assistance factors, such as the Alk5 inhibitor, HDAC inhibitor, and phosphoinositide-dependent protein kinase-1 inhibitor.

In some embodiments, cells that are not reprogrammed will not be viable in the reprogramming media within one week after initial exposure to the media. In other embodiments, the cells that are not reprogrammed will not be viable in the reprogramming growth media. Reprogramming growth media is media in which the reprogramming-assistance factors have not been added but FGF-2 and TGF-β have been added. In some cases, all the cells that are not reprogrammed will have died within 22 days of initial exposure of the cells to reprogramming media. When all the cells that have not been reprogrammed have died, the number of colonies can be counted to calculate the reprogramming efficiency. Each colony of cells may be presumed to have originated from a single reprogrammed cell that has divided to generate a colony if the number of cells are plated with a sufficient dilution such that the colonies originating from separate reprogrammed cells do not grow into one another. It is therefore contemplated that the practitioner titrate the plating of the cells after transfection and before placing the cells in the reprogramming media so that the reprogrammed and viable cells do not touch one another, and are sufficiently separated so that the individual colonies do not grow together. By titrating and plating several dilutions of cells after transfection, the practitioner can validate the colony counts across a range of titrations to ensure that the colony counts are consistent, and reflect the number of cells with plating. If the number of colonies counted are lower for more concentrated titrations, then each colony may not have originated from a single reprogrammed cell, and the practitioner should exclude the concentrated titrations and rely instead on titrations with a lower concentration of cells initially plated. IPSC reprogramming efficiency (expressed as a percentage) is defined by the following formula: number of colonies counted per 100,000 input cells×100.

In some embodiments, the reprogramming efficiency is greater than 0.0006%. In some embodiments, the reprogramming efficiency is greater than 0.001%. In some embodiments, the reprogramming efficiency is greater than 0.003%.

EXAMPLES Example 1: Generation of Adherent Cells and Vector Constructs

Cultured neonatal foreskin fibroblasts were isolated from discarded foreskin obtained by routine circumcisions through an approved Institutional Review Board (IRB) approved informed consent. Isolated cultured cells were de-identified in accordance with IRB procedures.

Each vector is based on the pCEP-4 episomal vector, SEQ ID NO: 20, previously developed by ThermoFisher Scientific (FIG. 1). Each vector contains an Epstein Barr virus origin of replication (OriP) as set forth in SEQ ID NO: 11, SV40 poly-adenylation sequence represented by SEQ ID NO: 19, 2A cleavage sequence for tandem genes, a bacterial origin of replication, as well as ampicillin and hygromycin resistance genes. There were seven separate vectors, which encode for a unique single reprogramming gene or tandem reprogramming genes separated by a 2A cleavage sequence, as illustrated in FIG. 1. Each vector either contains a single gene or tandem genes separated by a 2A cleavage sequence. In addition to the traditional Yamanaka factors (Oct-3/4, Sox-2 and Klf-4), there are separate vectors containing l-Myc along with Lin28, along with separate episomal vectors that encodes for p53 anti-sense and c-Myc. The system also contains a vector that encodes for Red Fluorescent Protein to monitor gene delivery and to detect silencing of exogenous reprogramming-assistance factors. Lastly, for each of the vectors to efficiently remain in the cell cytoplasm for only a short time frame, the plasmid vector encodes for Epstein Barr Nuclear Antigen-1 (EBNA-1).

Example 2: Transfection of Different Mixtures of Vector Constructs

One group of cultured human foreskin fibroblast (HFF) cells was reprogrammed with an additional vector that contained L-Myc and Lin28 separated by a 2A cleavage sequence. A separate group of cultured HFF cells was reprogrammed with an additional vector that encoded for the gene that expressed c-Myc. Lastly, one group of cultured HFF cells was reprogrammed without Myc and Lin28. Each condition contained a mixture of vectors that contain genes that encode for Oct3/4, Sox2, Klf-4, EBNA-1, p53 anti-sense and red fluorescent protein (RFP). FIG. 2 summarizes the different combination of specific vectors and reprogramming factors for the following conditions: 1) Oct3/4, Sox2, Klf-4, EBNA-1, p53 anti-sense, and RFP; 2) Oct3/4, Sox2, Klf-4, EBNA-1, p53 anti-sense, RFP, l-Myc and Lin28; and 3) Oct3/4, Sox2, Klf-4, EBNA-1, p53 anti-sense, RFP, and c-Myc. In other conditions, plasmids encoding EBNA-1, Sox-2, Klf-4 or Oct-3/4 were omitted from the combination of the specific vectors. In each condition, equal weights (μg) of each plasmid were combined to a total of 3.5 μg of DNA of the episomal reprogramming mix. FIG. 3 includes different polynucleotide and amino acid sequences for use in methods as disclosed herein, including for example, DNA that can be included in the pCEP-4 plasmid as vector constructs N1-7 in FIG. 1, the amino acid sequences translated therefrom, the OriP DNA sequence to which EBNA-1 binds, and the SV40 poly-adenylation sequence in the pCEP-4 plasmid. Additionally, FIG. 3 also shows DNA sequences and amino acid sequences for p53 from mouse.

Example 3: Timeline for Culturing and Preparation of Adherent Cells for Transfection

A temporal sequence of the IPSC reprogramming and cell expansion process is depicted in FIG. 4. Prior to transfection, a 6-well dish was coated with Vitronectin-XF according to manufacturer's directions (Primorigen, Madison, Wis.). HFF cells were examined under a microscope to ensure logarithmic growth phase and 80% confluency. HFF cells were washed with 1× Dulbecco's Phosphate Buffered Saline (ThermoFisher Scientific, Waltham, Mass.). TIFF cells were then exposed to 0.25% Trypsin-EDTA (ThermoFisher Scientific, Waltham, Mass.) and incubated at 37° Celsius for 4 minutes. When the cells were no longer adherent, an equal amount of 10 percent fetal bovine serum containing IMF growth media without antibiotics/anti-fungals was added. JIFF cells were counted and the density was adjusted to 1×10⁵ cells/mL. HFF cells were spun to pellet at 200×G for 5 minutes. Each cell pellet, containing 1×10⁵ cells/mL, was resuspended in 100 of Neon Electroporation Buffer R (ThermoFisher Scientific, Waltham, Mass.).

Example 4: Transfection

All the cultured conditions were electroporated and sequentially exposed to an IPSC reprogramming media followed by IPSC growth media in accordance with the timeline illustrated in FIG. 4. In brief, 3.5 μg of DNA of the episomal reprogramming mix was added to each tube and mixed gently. A Neon Electroporation Tip-100 was used to introduce the cells to the DNA. Using Buffer E2 for the chamber buffer, the cells were electroporated at 1650 V for 10 milliseconds for 3 cycles. Immediately after electroporation, the cells were placed in HFF growth media containing no antibiotics/antifungals on the previously coated 6-well dish for the first 24. Alternatively, another group of cells were transfected with a chemical mediated transfection, Lipofectamine LTX (ThermoFisher Scientific, Waltham, Mass., Catalog No. 15338100), using the manufacturer's protocol. Efficiency of gene transfer was measured by red fluorescence protein expression 48 hours post-transfection. RFP protein was expressed in cis with genes required for IPS reprogramming.

Example 5: Culturing in Reprogramming Media with Reprogramming-Assistance Factors

After 24 hours, the growth media was withdrawn and replaced with Cellular Engineering Technologies commercial IPSC reprogramming media (Catalog No. CET.IPS.RPM-250 containing antibiotics/antifungals). IPSC Reprogramming media comprised 1×DMEM/F12 with HEPES (ThermoFisher Scientific, Waltham, Mass.), 1×N-2 Supplement (ThermoFisher Scientific, Waltham, Mass.), 1×B-27 Supplement (ThermoFisher Scientific, Waltham, Mass.), 1×MEM Non-Essential Amino Acids (ThermoFisher Scientific, Waltham, Mass.) 1× Glutamax ((ThermoFisher Scientific, Waltham, Mass.)) and 1× Beta-Mercaptoethanol (ThermoFisher Scientific, Waltham, Mass.). The IPSC Reprogramming media was admixed with the following reprogramming-assistance factors: Sodium Butyrate (Reagents Direct, Encinitas, Calif.), A83-0-1 (Reagents Direct, Encinitas, Calif.), and PS48 (Reagents Direct, Encinitas, Calif.), and further admixed with ascorbic acid (Sigma-Aldrich, St. Louis, Mo.) and Human Recombinant FGF-2 (Peprotech, Rocky Hill, N.J.). To evaluate successful transfection, cells were examined under a microscope to detect RFP fluorescence within the first 48 hours after transfection. Both cells transfected via nucleofection and those transfected via Lipofectamine LTX transfected fluoresced more under the RFP excitation and emission wavelengths than untransfected controls, demonstrating successful introduction of and expression of the plasmids into the HFF cells. Cells were fed with fresh IPSC reprogramming media containing the above reprogramming-assistance Factors, FGF-2, and ascorbic acid every 48 hours through day 14 of the reprogramming process. By day 14, IPSC colonies were typically formed as shown under phase microscopy (FIG. 5A). Cultured cells were then switched to a xeno-free, feeder-free, growth media for an additional 7 days (Cellular Engineering Technology Catalog No. CET.IPS.RPM-250) without reprogramming-assistance Factors but with FGF-2 and a full media replacement was performed every 24 hours. Mature IPS colonies were observed starting around day 17 post electroporation, which displayed sharp and distinct borders. The identity of the IPS colonies was confirmed with positive probes for various IPSC markers including SSEA-4 Live Stain (ThermoFisher Scientific, Waltham, Mass., discontinued; Stemgent, Cambridge, Mass. Catalog No. 09-0097) and Alkaline Phosphatase (Catalog No. 00-0055, Stemgent, Cambridge, Mass.). By day 22 the number of colonies were counted and stained with alkaline phosphatase or SSEA4 livestain.

Example 6: Histological Staining/Fluorescence and Immunocytochemistry Staining/Fluorescence for IPSC Markers

Alkaline phosphatase stain (Stemgent, Cambridge, Mass.) and SSEA-4 livestain were conducted in accordance with the manufacturer's protocol. For fluorescence Immuno-cytochemistry for Nanog, Oct-3/4, and IRA160, cells were first fixed under 4% paraformaldehyde at a pH of 7.4, and washed subsequently with phosphate buffered saline (PBS), 3 times for 10 minutes each. Cells were permeabilized under PBS with 0.1% by volume Triton (PBS-0.4% T) overnight, and then blocked with PBS-0.1% T containing 1% by weight bovine serum albumin and 10% by volume normal goat serum. Then anti-Nanog conjugated with ALEXAFLOUR®488 (Abcam, Cat. No. ab196155), anti-Oct-3/4 conjugated with ALEXAFLOUR®488 (Abcam, Cat. No. ab208272), or anti-TRA160 (Abcam Cat. No. ab16288) were each applied at a 1:500 dilution (v:v) in PBS-0.1% T containing 0.5% by weight bovine serum albumin and 5% by volume normal goat serum and washed five times in PBS-0.1% T for 15 minutes each. For the anti-TRA160 ICC, anti-mouse antibody conjugated with ALEXAFLOUR®488 was applied at a 1:500 dilution (v:v) in PBS-0.1% T containing 0.5% by weight bovine serum albumin and 5% by volume normal goat serum and washed five times in PBS-0.1% T for 15 minutes each. All the slides were then coverslipped and imaged on a Olympus Fluorescent BX43 microscope using CellSens Software

Example 7: Statistical Testing

IPSC reprogramming efficiency (expressed as a percentage) was defined by the following formula: number of colonies counted per 100,000 input cells×100. Data are reported as means±SE. Comparisons between more than two groups were made with analysis of variance. Individual group comparisons were done with Tukey's honestly significant difference test for post hoc comparison of means. Differences were considered significant at the P<0.05 level.

Example 8: Morphology of and Markers for a Reprogrammed IPSC from Somatic Cells

By day 14, IPSC colonies were typically formed as shown under phase microscopy (FIG. 5A). Colonies exhibit the typical flat shape and refractile border. IPSC colonies also stain positive for alkaline phosphatase (FIG. 5B) and also express SSEA4 (FIG. 5C), confirming the process resulted in fully reprogrammed cells. Additionally, representative colonies depicted by phase microscopy and other pluripotent biomarkers (Nanog, Oct4 and TRA160) were observed within the same corresponding colony (FIG. 5D).

Example 9: Loss of Episomal Vectors and/or Expression of Genes from Episomal Plasmids after Two Weeks

Lack of red fluorescent protein (RFP) expression in the IPSC colonies (FIGS. 6A-6B.) confirms that the episomal vectors cease expression at day 17. As shown in the FIG. 6A, there are two IPSC colonies that are highlighted under phase microscopy at day 17. The corresponding fluorescent images (FIG. 6B) show that the IPSC colonies no longer express RFP, which indicate that the genes encoded by the episomal vectors had shutdown.

Example 10: Effect of Reprogramming-Assistance Factors on Reprogramming Efficiency of Somatic Cells

Next, the numbers of colonies generated between the different vector constructs were compared among cultured cells reprogrammed in the presence and absence of reprogramming-assistance factors (FIGS. 7A-7B). When the vector mixtures are transfected in cultured cells in the absence of reprogramming-assistance factors, there are 0 to 1 colony detected (FIG. 7B) irrespective whether in the presence or absence of Myc-dependent and Lin28 transcriptional factors. When the vector-transfected cells were then cultured with reprogramming-assistance factors (FIG. 7A), the number of colonies significantly increased. Within cells cultured with reprogramming media, transfection with either l-Myc combined with Lin28 or c-Myc increases the number of colonies surviving compared to transection with EBNA-1, Sox-2, KLF-4, and Oct-3/4 genes and p53-antisense alone. There was no statistically significant difference in the number of colonies formed between cells transfected with l-Myc combined with Lin28 and those transfected with c-Myc. Omission of any one of EBNA-1, Sox-2, KLF-4, or Oct-3/4 from the transfection prevents all colony formation, regardless of whether c-Myc or Lin28 were also transfected. These observations were consistent regardless if c-Myc or Lin28 were included or not. Thus, all four reprogramming-assistance factors were necessary to mediate efficiently form IPSC using this episomal reprogramming system.

Example 11: Effect of L-Myc/Lin28, c-Myc, and Oncogene-Free Conditions on Reprogramming Efficiency

When expressed as the percentage of colonies counted per 100,000 of input cells, there was a parallel significant difference in the reprogramming efficiency between cells transfected in the presence and absence of Myc-dependent and Lin28 transcriptional factors (FIG. 8). Interestingly, cultured cells transfected with c-Myc resulted in a statistically higher reprogramming efficiency than cultured cells transfected with l-Myc combined with Lin28.

Example 12: Effect of L-Myc/Lin28, c-Myc, and Oncogene-Free Conditions on Reprogrammed Cells Expressing SSEA4

Next, reprogramming efficiency was further quantified by measuring the fraction of colonies that expressed SSEA4 when exposed to reprogramming factors. As shown in FIG. 9, all the colonies were fully reprogrammed irrespective of whether the cells were transfected in the presence or absence of Myc-dependent and Lin28 transcriptional factors (standard error=0). Taken together, the data demonstrate that the approach of combining reprogramming factors with mixtures of episomal vectors that lacked Myc and Lin28 and SV40 large T antigen created IPSC colonies which were all fully reprogrammed.

While the transfection of l-Myc and c-Myc mediated an anticipated greater number of colonies than in the absence of these genes, all transfections groups, including those treated in the absence of c-Myc and l-Myc expression vectors, yielded colonies in which 100 percent were fully reprogrammed based on the expression of SSEA4.

The present results demonstrate efficient episomal reprogramming in the absence of either SV40 large T antigen, or Nanog. Reprogramming could also be achieved with efficient results, albeit at a lower efficiency, in the absence of oncogenes, c-Myc, l-Myc, and Lin28.

To confirm that the SSEA4 expressing colonies contained fully reprogrammed IPSCs, the induced pluripotent cells derived from fibroblasts were then exposed to various factors to trigger their differentiation into: 1) ectodermal cells, such as neural precursor cells; 2) mesodermal cells, such as heart muscle cells; and 3) endodermal cells.

Example 13: IPSCs Derived from HFF Cells can Differentiate into Cardiomyocytes, a Mesodermal Cell

For differentiation of IPSCs into neural progenitor cells, IPSCs were first washed in pre-warmed 1× Dulbecco's Phosphate Buffered Saline (DPBS); DPBS was then removed, and 1× Versene at room temperature was added to the IPSCs, and cells were allowed to rest for 10 min Thereafter, the 1× Versene is removed and Cellular Engineering Technology's IPSC growth media is added. Cells are triturated to create cell clumps of approximately 100-200 cells and are plated onto a 3.5 cm round bottom dish which was previously coated for 1 hour with 1 mL of 10 μg/mL Vitronectin XF and then washed with CellAdhere™ buffer.

After two days, room-temperature Cellular Engineering Cardiomyocyte Differentiation Media was mixed by adding 2 mL of the Step 2 supplement into Cardiomyocyte Differentiation Step 2 and 4 Base Media. The IPSC growth media was removed and replaced with 2 mL of the Cardiomyocyte Differentiation Step 2 and 4 Media premixed with the Step 2 supplement. After 24 hours of incubation at 37° C., Cardiomyocyte Differentiation Step 3 media was prepared by mixing 2 mL of the Cardiomyocyte Differentiation Step 3 supplement with the Cardiomyocyte Differentiation Step 3 Base Media. Thereafter, the Cardiomyocyte Differentiation Media Step 2 and 4 was removed from the cells and replaced with 2 mL of the premixed Cardiomyocyte Differentiation Step 3 Media premixed with Step 3 supplement. Cells were then incubated at 37° C. for 2 days. Next, the Cardiomyocyte Differentiation Step 3 Media was removed and replaced with 2 mL of the premixed Cardiomyocyte Step 2 and 4 Media premixed with the Step 2 supplement. Cells were then incubated at 37° C. for 2 days. Thereafter, Cardiomyocyte Differentiation Step 5 Media was made by combining 2 mL of the Step 5 supplement with the Cardiomyocyte Differentiation Step 5 Base Media, and the Cardiomyocyte Step 2 and 4 Media was removed from the cells and replaced with 2 mL of the premixed Cardiomyocyte Differentiation Step 5 Media. Cells were then incubated at 37° C. for 2 days. Thereafter, cells were fed every 48 hours by replacing the media with unused premixed Cardiomyocyte Differentiation Step 5 Media for four days.

Thirteen days after first passage of the cells, or 4 days after initial exposure to the Cardiomyocyte Differentiation Step 5 Media, the cells beat or contract in a pulsatile pattern. Cells were then fixed under 4% paraformaldehyde and immunocytochemistry for troponin and/or stained with fluorescent phalloidin which binds to and detects filamentous-actin (F-actin). FIG. 10 depicts fluorescent-phalloidin-stained cardiomyocytes (phalloidin stain is green) derived from IPSCs which were in turn derived from HFF. FIG. 11 depicts fluorescent-anti-troponin-stained cardiomyocytes wherein a green fluorophore conjugated secondary antibody was bound to the troponin antibody and the cells were derived from IPSCs which were in turn derived from HFF. The presence of phalloidin-fluorescent and troponin-fluorescent cells demonstrate that HFF cells can be reprogrammed into IPSCs because the IPSCs have the capacity to differentiate into cardiomyocytes, which is a mesoderm-derived cell. Additionally, these cells beat or contracted in a regular pulsatile manner demonstrating that the cells express hyperpolarization-activated cyclic nucleotide-gated channels which trigger an actin-myosin-mediated contraction, a mechanism only found in cardiomyocytes.

Example 14: IPSCs Derived from HFF Cells can Differentiate into Brachyury Positive Mesodermal Cell

For differentiation of IPSCs into mesoderm cells, IPSCs were first washed in pre-warmed 1× Dulbecco's Phosphate Buffered Saline (DPBS); DPBS was then removed, and 1× Versene at room temperature was added to the IPSCs, and cells were allowed to rest for 10 min. Thereafter, the 1× Versene was removed and Cellular Engineering Technology's IPSC growth media was added. Cells were triturated to create cell clumps of approximately 100-200 cells and were plated onto a 3.5 cm round bottom dish previously coated with 1.44 mL-1.92 mL of Matrigel (Corning Cat. No. 356234).

Cells were placed in an incubator at 37° C., 95% humidity, and 5% CO₂ for 24 hours, and then fed by replacing the IPSC Growth Media with fresh IPSC Growth Media every 24 hours until 85% to 90% confluency on the plate surface is met. Then, Cellular Engineering Technology's Mesoderm Differentiation Media (Catalog No. CET.DIFF.MDM-250) is made by mixing 10 mL of Cellular Engineering Technology's Mesoderm Supplement with Cellular Engineering Technology's Mesoderm Base Media. The IPSC Growth Media was immediately with 2 mL premixed Cellular Engineering Technology's Mesoderm Differentiation Media at room temperature, and placed back into the 37° C. incubator. Cells were then fed every 48 hours by replacing the premixed Cellular Engineering Technology's Mesoderm Differentiation Media on the cells with fresh premixed Cellular Engineering Technology's Mesoderm Differentiation Media at room temperature, and placing the cells back in the 37° C. incubator.

After 4 days in premixed Cellular Engineering Technology's Mesoderm Differentiation Media, the cells were fixed with 4% paraformaldehyde and fluorescent immunocytochemistry for brachyury protein using the antibody manufacturer's protocol. See for example Santa Cruz Biotechnology, Inc. brachyury N-19 antibody (Catalog No. SC-17743) available at, for example, www.scbt.com/scbt/product/brachyury-antibody-n-19. FIG. 12 depicts anti-brachyury-fluorescent cardiomyocytes wherein a green fluorophore conjugated secondary antibody is bound to the anti-brachyury antibody, and the cells were derived from IPSCs which were in turn derived from HFF. The presence of brachyury-fluorescent cells demonstrate that HFF cells can be reprogrammed into IPSCs because the IPSCs have the capacity to differentiate into mesoderm cells.

Example 15: IPSCs Derived from HFF Cells can Differentiate into Neural Progenitor Cells, an Ectodermal Cell

For differentiation of IPSCs into neural progenitor cells, IPSCs were first washed in pre-warmed 1× Dulbecco's Phosphate Buffered Saline (DPBS); DPBS was then removed, and 1× Versene at room temperature was added to the IPSCs, and cells were allowed to rest for 10 min Thereafter, the 1× Versene was removed and Cellular Engineering Technology's IPSC growth media was added. Cells were triturated to create cell clumps of approximately 100-200 cells and were plated onto a 3.5 cm round bottom dish previously coated with 1.44 mL-1.92 mL of Matrigel (Corning Cat. No. 356234).

After two days, room-temperature Cellular Engineering Technology's Neural Progenitor Cell Induction Media (Catalog No. CET.DIFF.NPCM-250), was prepared by adding 16 mL of the Cellular Engineering Technology's Neural Progenitor Supplement to the Cellular Engineering Technology's Neural Progenitor Base Media. The IPSC growth media was removed from the IPSCs and 2 mL of the pre-mixed, room-temperature Cellular Engineering Technology's Neural Progenitor Cell Induction Media was added. The media was then replaced daily for four days with another 2 mL of pre-mixed, room-temperature Cellular Engineering Technology's Neural Progenitor Cell Induction Media.

Cells were then fixed with 4% paraformaldehyde and immunocytochemistry was performed for neural progenitor cell markers PAX-6 and/or Nestin. FIG. 13 depicts fluorescent-nestin positive neural progenitor cells derived from IPSCs which were in turn derived from HFF. FIG. 14 depicts fluorescent-PAX-6 positive neural progenitor cells derived from IPSCs which were in turn derived from HFF. The presence of fluorescent-nestin and fluorescent-PAX-6-stained cells demonstrates that HFF cells can be reprogrammed into IPSCs because the IPSCs have the capacity to differentiate into ectodermal cells such as neural progenitor cells.

Example 16: IPSCs Derived from HFF Cells can Differentiate into Definitive Endodermal Cell

For differentiation of IPSCs into endoderm cells, IPSCs were first washed in pre-warmed 1× Dulbecco's Phosphate Buffered Saline (DPBS); DPBS was then removed, and 1× Versene at room temperature was added to the IPSCs, and cells were allowed to rest for 10 min. Thereafter, the 1× Versene was removed and Cellular Engineering Technology's IPSC growth media was added. Cells were triturated to create cell clumps of approximately 100-200 cells and were plated onto a 3.5 cm round bottom dish previously coated with 1.44 mL-1.92 mL of Matrigel (Corning Cat. No. 356234). Cells were placed in an incubator at 37° C., 95% humidity, and 5% CO₂ for 24 hours, and then fed by replacing the IPSC Growth Media with fresh IPSC Growth Media every 24 hours until 85% to 90% confluency on the plate surface is met.

After two days, room-temperature Cellular Engineering Technology's Definitive Endoderm Differentiation Media (Catalog No. CET.DIFF.DEM-250) was prepared by adding 10 mL of Cellular Engineering Technology's Definitive Endoderm Supplement to the Cellular Engineering Technology's Definitive Endoderm Base Media. The IPSC growth media was removed from the IPSCs and 2 mL of the pre-mixed, room-temperature Cellular Engineering Technology's Definitive Endoderm Differentiation Media was added. Cells were then fed every 48 hours by replacing the premixed Cellular Engineering Technology's Definitive Endoderm Differentiation Media on the cells with fresh premixed Cellular Engineering Technology's Definitive Endoderm Differentiation Media at room temperature, and placing the cells back in the 37° C. incubator.

After 4 days in premixed Cellular Engineering Technology's Definitive Endoderm Differentiation Media, the cells were fixed with 4% paraformaldehyde and fluorescent immunocytochemistry for SOX-17 and/or FOXA2 protein using the antibody manufacturer's protocol. See for example Santa Cruz Biotechnology, Inc. SOX-17 3.5CH antibody (Catalog No. SC-130295) available at, for example, www.scbt.com/scbt/product/sox-17-antibody-3-5ch. See also for example Abcam, Inc. FOXA2 antibody EPR4466 (Catalog No. ab108422) available at, for example, www.abcam.com/foxa2-antibody-epr4466-ab108422.html. FIG. 15 depicts anti-SOX-17-fluorescent endoderm cells wherein a green fluorophore conjugated secondary antibody is bound to the SOX-17 antibody, and the cells were derived from IPSCs which were in turn derived from HFF. FIG. 16 depicts anti-FOXA2-fluorescent endoderm cells wherein a green fluorophore conjugated secondary antibody is bound to the FOXA2 antibody, and the cells were derived from IPSCs which were in turn derived from HFFs. The presence of SOX-17-fluorescent cells and FOXA2-fluorescent cells demonstrate that HFF cells can be reprogrammed into IPSCs because the IPSCs have the capacity to differentiate into definitive endoderm cells. Because the same SSEA4-positive reprogrammed cells derived from HFFs could differentiate into mesodermal, ectodermal, and endodermal cells, the SSEA4-positive reprogrammed cells derived from HFFs are pluripotent.

Example 17: Isolation of Mononuclear Cells from Cord Blood and Peripheral Blood

Cultured neonatal mononuclear cells were isolated from discarded cord blood. Cord blood was obtained under an informed consent from parents that underwent routine normal deliveries from a local hospital. Additionally, five milliliters of whole blood were obtained by venipuncture from a 7-year-old male Cystic Fibrosis patient that carried a homozygous delta 508 mutation. A similar amount of blood was obtained from a 57-year-old female with A1ATD carrying a ZZ-phenotype. Clinical procedures were approved by the John Paul II Medical Research Institute Institutional Review Board (IRB). Isolated cultured cells were de-identified in accordance with IRB procedures such that researchers that processed tissue samples were not aware of the donor's identity. Whole blood was collected during venipuncture using standard vacutainer tubes containing EDTA. Whole blood was diluted 1:1 using Dulbecco's Phosphate Buffered Saline (DPBS). PBMC's were isolated using the Ficoll-Paque technique density based centrifugation. Briefly, 16 mL of Ficoll-Paque solution was pipetted into a Leucosep Tube. The tube was spun at 1000×g for 30 seconds at 20° C. The Ficoll-Paque was located below the porous barrier. The diluted whole blood was layered above the Styrofoam frit in the Leucosep tube and the sample was spun at 1000×g for 10 minutes at 20° C. The middle (white) layer, consisting of PBMC's, was collected using a serological pipette. The collected layer was mixed with an equal volume of DPBS, mixed and centrifuged at 300×g for 10 minutes at 20° C. The supernatant was aspirated and cells were resuspended in 300 microliters of DPBS and counted using a Millipore Scepter counter.

PBMCs were then exposed to hematopoetic stem cell media (HSC) differentiation media with antibiotics for 7 days. Next, cells were placed into HSC differentiation media without antibiotics and were electroporated according to Examples 2 and 4 above. After 24 hours, cell media was changed to HSC media with antibiotics, and the HSC media with antibiotics was replaced again after 24 hours (2 days after transfection). Three days after transfection, the media was replaced with Reprogramming media. IPSC Reprogramming media comprised 1×DMEM/F12 with HEPES (ThermoFisher Scientific, Waltham, Mass.), 1×N-2 Supplement (ThermoFisher Scientific, Waltham, Mass.), 1×B-27 Supplement (ThermoFisher Scientific, Waltham, Mass.), 1×MEM Non-Essential Amino Acids (ThermoFisher Scientific, Waltham, Mass.) 1× Glutamax ((ThermoFisher Scientific, Waltham, Mass.)) and 1× Beta-Mercaptoethanol (ThermoFisher Scientific, Waltham, Mass.). The IPSC Reprogramming media was admixed with the following reprogramming-assistance factors: Sodium Butyrate (Reagents Direct, Encinitas, Calif.), A83-0-1 (Reagents Direct, Encinitas, Calif.), and PS48 (Reagents Direct, Encinitas, Calif.), and further admixed with ascorbic acid (Sigma-Aldrich, St. Louis, Mo.) and Human Recombinant FGF-2 (Peprotech, Rocky Hill, N.J.). Cells were fed every 48 hours, replacing the old IPSC Reprogramming media containing the above Reprogramming-assistance factors, FGF-2, and ascorbic acid. Fourteen days after transfection, the media was then replaced with IPSC Reprogramming media without the above reprogramming-assistance factors but with FGF-2, until 22 days after transfection. At 22 days after transfection, the cells were subjected to experiments in Examples 18-22 below and were exposed to immunofluorescence labeling for Nanog, Oct-3/4, TRA160, and SSEA-4 Live Stain (ThermoFisher Scientific, Waltham, Mass., discontinued; Stemgent, Cambridge, Mass. Catalog No. 09-0097) and Alkaline Phosphatase (Catalog No. 00-0055, Stemgent, Cambridge, Mass.) as in Example 5 above. FIG. 17 depicts the timeline of the PBMCs to HSC media, transfection, and reprogramming media with and without reprogramming-assistance factors described above. FIG. 18 depicts colonies immunofluorescent for Nanog, Oct-3/4, TRA160, and positive for SSEA-4 Live Stain and Alkaline Phosphatase stain after being reprogrammed into IPSC with episomal vectors free of Myc and Lin28 and cultured in IPSC reprogramming media in the presence of IPSC reprogramming-assistance factors, PS48, A83-01, and sodium butyrate, and HSC differentiation media.

Example 18: Flow Cytometry

Flow cytometry was conducted using a Guava EasyCyte HT. Cells were dissociated using Trypsin Like Enzyme (Tryp-LE) for 10 minutes at 37° C. Dissociated cells were pipetted to remove aggregations and clumps and passed through a 70-micron filter. Single cell suspensions were counted using a Millipore Scepter counter and cell density was adjusted to 1×10⁵ cells/100 microliters. 5 microliters of appropriate antibody was added to the dissociated cells and mixed using gentle pipetting. This was then incubated in the dark for 30 minutes on ice. At the end of this incubation period, labeled cells were washed with 1× ice cold DPBS and resuspended in 200 microliters DPBS. Cells were then counted using a Guava EasyCyte HT. Viable cells were gated using a log/log Forward Scatter/Side Scatter plot. Each IPSC marker fluorescence was also compared to its IgKappa Isotype control to quantify non-specific and autofluorescence events. Each IPSC marker was counted and plotted as a graph with the abscissa containing the log Fluorescence of a given marker and the ordinate containing the counts of either a negative or positive viable gated cell. This graph was then used to create histograms providing percentages of negative and positive cells. Based on the IgKappa Isotype control, 10² was used as the cutoff in log Fluorescence between a negative and a positive cell.

Example 19: Morphology of IPSC Colonies Derived from CBDMNCs

Myc/Lin28-free IPSC colonies derived from CBDMNC exhibited the typical flat shape and retractile border as shown under phase microscopy (FIG. 18). IPSC colonies also stain positive for alkaline phosphatase (FIG. 18). Colonies also expressed pluripotent biomarkers that include SSEA4, Nanog, Oct4 and TRA160 (FIG. 18), which confirm that the reprogramming process resulted in fully reprogrammed cells.

Example 20: Effect of Reprogramming-Assistance Factors on IPSC Colony Formation from CBDMNCs

HSC differentiation was necessary to reprogram CBDMNC into IPSC. The number of colonies were measured in c-Myc, l-Myc/Lin28 and Myc/Lin28-free groups pretreated in the presence and absence of HSC differentiation media. There was IPSC colony formation in all three groups pretreated with HSC differentiation media. There were statistically more observed colonies in cells treated with Myc and Lin28 than in Myc/Lin28-free cells (FIG. 19). However, there were no observed colonies in groups that were not pretreated with HSC differentiation media regardless in the presence and absence of Myc/Lin28. Taken together, these data indicate that CBDMNC conversion into IPSC required preceding HSC differentiation.

Example 21: Flow Cytometry of CBDMNC after HSC Conversion to Generate CD34+ Cells

HSC conversion from CBDMNC was further quantitated by flow cytometry. Cultured CBDMNC were exposed to 7 days of HSC differentiation media and the amount of HSC were quantified by an antibody against human CD34+ cell expression. A dot blot is illustrated in FIG. 20A which identified two separate population CD34+ cells and CD34− cells. FIG. 20B depicts a histogram which demonstrated that 13 percent of CBDMNC cells are converted into CD34+ cells. In contrast, CD34+ cells represented only 1 percent of the unstimulated cultured CBDMNC (FIG. 20C). These results indicate that CD34+ cell expression is required before IPSC reprogramming. Further, these results indicate only a small a fraction of the total cellular population is necessary to achieve IPSC conversion.

Example 22: Effect of the Number of Input CBDMNCs and c-Myc, or L-Myc+Lin28, or Oncogene Free Conditions on Reprogramming

An observed dose-dependent increase in colony number as a function of input cell number. The number of IPSC colonies were compared in CBDMNC transformed in the presence and absence of Myc and Lin28 (FIG. 21) at input cell number between 100,000 and 1,000,000. There were no IPSC colonies formed at 100,000 input cells. A minimum of 300,000 input cells was necessary to produce IPSC colonies regardless of whether Myc/Lin28 was used or not. We also observed a statistically higher number of colonies with input cell numbers of 500,000 and 1,000,000 than at input cell numbers of 300,000 cells regardless of the presence or absence of Myc and Lin28. Further, there was a statistically significant difference in the number of colonies between Myc/Lin28 treated cells and cultured cells treated in the absence of these oncogenes (FIG. 21).

Moreover, the reprogramming efficiency was observed at a maximum at 300,000 input cells when expressed as the number of colonies per number of CBDMNC input number×100 (FIG. 22) regardless of whether reprogrammed in the presence or absence of Myc/Lin28. As anticipated, the reprogramming efficiency was statistically higher in CBDMNC that were reprogrammed with Myc and Lin28 than in the absence of these oncogenes.

Despite the differential colony counts and reprogramming efficiency in CBDMNC treated in the presence and absence of Myc/Lin28, there was no significant difference in the percentage of colonies that were fully reprogrammed. Based on the expression of SSEA4, 100 percent of all colonies expressed SSEA4 with a standard error (FIG. 23). These effects were observed at input cells of 300,000, 500,000 and 1,000,000. Taken together with the results of FIG. 22, there was no advantage in reprogramming efficiency with cultured CBDMNC at cell input numbers that exceeded 300,000 cells.

Example 23: Reprogramming of Peripheral Blood MNC from 57-Year-Old with Alpha1 Antitrypsin Deficiency with a PiZZ Phenotype

Peripheral blood MNC cells from a 57-year-old Caucasian female with alpha 1 antitrypsin deficiency with a PiZZ phenotype were reprogrammed into IPSC with episomal vectors free of Myc and Lin28 and HSC differentiation media using the protocols and materials of Examples 17 above. FIG. 24 depicts colonies captured 14 days after transfection. Typical IPSC colony depicted by phase contrast microscopy. Representative IPSC colony stained positive for alkaline phosphatase. Representative IPSC colonies exhibited pluripotency by immunofluorescent live stain for SSEA4, Nanog, Oct4 and TRA160. Each panel is representative of 4 separate experiments. Scale bar represents 100 microns.

Example 24: Reprogramming of Peripheral Blood MNC from a 7-year-old with Cystic Fibrosis and a Delta 508 Mutation

Peripheral blood MNC cells from a 7-year-old Caucasian male with Cystic Fibrosis with the delta 508 mutation were reprogrammed into IPSC with episomal vectors free of Myc and Lin28 and HSC differentiation media using the protocols and materials of Examples 17 above. FIG. 25 depicts colonies captured 14 days after transfection. Representative image of an entire culture stained with alkaline phosphatase. Representative IPSC colony stained for alkaline phosphatase. Representative IPSC colonies exhibited pluripotency by immunofluorescent live stain for SSEA4, Nanog, Oct4 and TRA160. Each panel is representative of 4 separate experiments. Scale bar represents 100 microns. 

What is claimed is:
 1. A method for reprogramming a somatic cell comprising: culturing a somatic cell comprising one or more non-integrating vectors encoding Sox-2, Klf-4, and Oct3/4 in a reprogramming medium comprising an exogenous Alk-5 inhibitor, an exogenous histone deacetylase inhibitor, an exogenous activator of glycolysis, and exogenous ascorbic acid; and obtaining an integration-free, virus-free, exogenous oncogene-free induced pluripotent stem (iPS) cell.
 2. The method for reprogramming a somatic cell according to claim 1, wherein the one or more non-integrating vectors also encode EBNA-1.
 3. The method for reprogramming a somatic cell according to claim 1, further comprising maintaining the obtained iPS cell in a dedifferentiation maintenance medium comprising basic fibroblast growth factor and transforming growth factor beta after being cultured in the reprogramming medium.
 4. The method for reprogramming a somatic cell according to claim 1, wherein the culturing does not require feeder cells.
 5. The method for reprogramming a somatic cell according to claim 1, wherein the Alk-5 inhibitor comprises 3-(6-Methyl-2-pyridinyl)-N-phenyl-4-(4-quinolinyl)-1H-pyrazole-1-carbothioamide (A83-01), 4-[4-(1,3-benzodioxol-5-yl)-5-(2-pyridinyl)-1H-imidazol-2-yl]benzamide, 4-[4-[3-(2-Pyridinyl)-1H-pyrazol-4-yl]-2-pyridinyl]-N-(tetrahydro-2H-pyran-4-yl)-benzamide, or 6-[2-(1,1-Dimethylethyl)-5-(6-methyl-2-pyridinyl)-1H-imidazol-4-yl]quinoxaline; the histone deacetylase inhibitor comprises sodium butyrate or valproic acid; and the activator of glycolysis comprises 5-(4-Chloro-phenyl)-3-phenyl-pent-2-enoic acid (PS48); α,α,-Dimethyl-4-[2-methyl-8-[2-(3-pyridinyl)ethynyl]-1H-imidazo[4,5-c]quinolin-1-yl]-benzeneacetonitrile (BAG956); N-[3-[[5-Iodo-4-[[3-[(2-thienylcarbonyl)amino]propyl]amino]-2-pyrimidinyl]amino]phenyl]-1-pyrrolidinecarboxamide (BX795); (3S,6R)-1-[6-(3-Amino-1H-indazol-6-yl)-2-(methylamino)-4-pyrimidinyl]-N-cyclohexyl-6-methyl-3-piperidinecarboxamide (GSK 2334470); 2-Amino-N-[4-[5-(2-phenanthrenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]phenyl]acetamide (OSU03012); or 4-Dodecyl-N-1,3,4-thiadiazol-2-yl-benzenesulfonamide (PHT427).
 6. The method for reprogramming a somatic cell according to claim 5, wherein the Alk-5 inhibitor comprises A83-01, the histone deacetylase inhibitor comprises sodium butyrate, and the activator of glycolysis comprises PS48.
 7. The method for reprogramming a somatic cell according to claim 1, wherein the somatic cell is a human cell and reprogramming efficiency exceeds 0.0006%.
 8. A composition comprising a somatic cell and a cell culture medium, the somatic cell comprising episomal polynucleotides encoding Sox-2, Klf-4, and Oct3/4, and the medium comprising an exogenous Alk-5 inhibitor, an exogenous histone deacetylase inhibitor, an exogenous activator of glycolysis, and exogenous ascorbic acid.
 9. The composition according to claim 8, wherein the somatic cell further comprises an episomal polynucleotide encoding EBNA-1.
 10. The composition according to claim 8, wherein the somatic cell is a human cell.
 11. The composition according to claim 8, wherein the medium or the somatic cell further comprises an agent for inhibiting p53 activity.
 12. The composition according to claim 11, wherein the agent for inhibiting p53 activity comprises a compound selected from pifithrin-α, cyclic pifithrin-α, pifithrin-μ, RITA, SJ 172550, nutlin-3, a pharmaceutically acceptable salt of one of the aforementioned compounds, or an antisense oligonucleotide.
 13. The composition according to claim 8, wherein the Alk-5 inhibitor comprises 3-(6-Methyl-2-pyridinyl)-N-phenyl-4-(4-quinolinyl)-1H-pyrazole-1-carbothioamide (A83-01), 4-[4-(1,3-benzodioxol-5-yl)-5-(2-pyridinyl)-1H-imidazol-2-yl]benzamide, 4-[4-[3-(2-Pyridinyl)-1H-pyrazol-4-yl]-2-pyridinyl]-N-(tetrahydro-2H-pyran-4-yl)-benzamide, or 6-[2-(1,1-Dimethylethyl)-5-(6-methyl-2-pyridinyl)-1H-imidazol-4-yl]quinoxaline; the histone deacetylase inhibitor comprises sodium butyrate or valproic acid; and the activator of glycolysis comprises 5-(4-Chloro-phenyl)-3-phenyl-pent-2-enoic acid (PS48); α,α,-Dimethyl-4-[2-methyl-8-[2-(3-pridinyl)ethynyl]-1H-imidazo[4,5-c]quinolin-1-yl]-benzeneacetonitrile (BAG956); N-[3-[[5-Iodo-4-[[3-[(2-thienylcarbonyl)amino]propyl]amino]-2-pyrimidinyl]amino]phenyl]-1-pyrrolidinecarboxamide (BX795); (3S,6R)-1-[6-(3-Amino-1H-indazol-6-yl)-2-(methylamino)-4-pyrimidinyl]-N-cyclohexyl-6-methyl-3-piperidinecarboxamide (GSK 2334470); 2-Amino-N-[4-[5-(2-phenanthrenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]phenyl]acetamide (OSU03012); or 4-Dodecyl-N-1,3,4-thiadiazol-2-yl-benzenesulfonamide (PHT427).
 14. The composition according to claim 13, wherein the Alk-5 inhibitor comprises A83-01, the histone deacytylase inhibitor comprises sodium butyrate, and the activator of glycolysis comprises PS48.
 15. A kit comprising: (a) one or more non-integrating vectors encoding Sox-2, Klf-4, and Oct3/4; (b) an Alk-5 inhibitor, (c) a histone deacetylase inhibitor, (d) an activator of glycolysis, and (e) ascorbic acid.
 16. The kit according to claim 15, wherein the one or more non-integrating vectors also encode EBNA-1.
 17. The kit according to claim 15, which further comprises an agent for inhibiting p53 activity.
 18. The kit according to claim 17, wherein the agent for inhibiting p53 activity comprises a compound selected from pifithrin-α, cyclic pifithrin-α, pifithrin-μ, RITA, SJ 172550, nutlin-3, a pharmaceutically acceptable salt of one of the aforementioned compounds, or an antisense oligonucleotide.
 19. The kit according to claim 15, wherein the Alk-5 inhibitor comprises 3-(6-Methyl-2-pyridinyl)-N-phenyl-4-(4-quinolinyl)-1H-pyrazole-1-carbothioamide (A83-01), 4-[4-(1,3-benzodioxol-5-yl)-5-(2-pyridinyl)-1H-imidazol-2-yl]benzamide, 4-[4-[3-(2-Pyridinyl)-1H-pyrazol-4-yl]-2-pyridinyl]-N-(tetrahydro-2H-pyran-4-yl)-benzamide, or 6-[2-(1,1-Dimethylethyl)-5-(6-methyl-2-pyridinyl)-1H-imidazol-4-yl]quinoxaline; the histone deacetylase inhibitor comprises sodium butyrate or valproic acid; and the activator of glycolysis comprises 5-(4-Chloro-phenyl)-3-phenyl-pent-2-enoic acid (PS48); α,α,-Dimethyl-4-[2-methyl-8-[2-(3-pridinyl)ethynyl]-1H-imidazo[4,5-c]quinolin-1-yl]-benzeneacetonitrile (BAG956); N-[3-[[5-Iodo-4-[[3-[(2-thienylcarbonyl)amino]propyl]amino]-2-pyrimidinyl]amino]phenyl]-1-pyrrolidinecarboxamide (BX795); (3S,6R)-1-[6-(3-Amino-1H-indazol-6-yl)-2-(methylamino)-4-pyrimidinyl]-N-cyclohexyl-6-methyl-3-piperidinecarboxamide (GSK 2334470); 2-Amino-N-[4-[5-(2-phenanthrenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]phenyl]acetamide (OSU03012); or 4-Dodecyl-N-1,3,4-thiadiazol-2-yl-benzenesulfonamide (PHT427).
 20. The kit according to claim 19, wherein the Alk-5 inhibitor comprises A83-01, the histone deacetylase inhibitor comprises sodium butyrate, and the activator of glycolysis comprises PS48. 